rs864687

Variant names:

• chr7-105565470-A-C
• rs864687
• NM_021930.6:c.2067+13A>C

Your query was ambiguous. Multiple possible variants found:

• chr7-105565470-A-C
• chr7-105565470-A-T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001355530.2(EFCAB10):​c.*79T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0678 in 1,612,222 control chromosomes in the GnomAD database, including 4,761 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.10 (1208 hom., cov: 33)
  • Exomes 𝑓: 0.064 (3553 hom.)
• Consequence: EFCAB10 NM_001355530.2 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -0.279
• Publications: 9 publications found

Genes affected

RINT1 (HGNC:21876): (RAD50 interactor 1) This gene encodes a protein first identified for its ability to interact with the RAD50 double strand break repair protein, with the resulting interaction implicated in the regulation of cell cycle progression and telomere length. The encoded protein may also play a role in trafficking of cellular cargo from the endosome to the trans-Golgi network. Mutations in this gene may be associated with breast cancer in human patients. [provided by RefSeq, Oct 2016]

EFCAB10 (HGNC:34531): (EF-hand calcium binding domain 10) Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 7-105565470-A-C is Benign according to our data. Variant chr7-105565470-A-C is described in ClinVar as Benign. ClinVar VariationId is 403379.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001355530.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RINT1	NM_021930.6	MANE Select	c.2067+13A>C		intron	N/A	NP_068749.3
	EFCAB10	NM_001355526.2	MANE Select	c.384-23T>G		intron	N/A	NP_001342455.1	A6NFE3
	EFCAB10	NM_001355530.2		c.*79T>G		3_prime_UTR	Exon 5 of 5	NP_001342459.1	J3KR52

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RINT1	ENST00000257700.7	TSL:1 MANE Select	c.2067+13A>C		intron	N/A	ENSP00000257700.2	Q6NUQ1
	EFCAB10	ENST00000480514.6	TSL:1 MANE Select	c.384-23T>G		intron	N/A	ENSP00000418678.1	A6NFE3
	EFCAB10	ENST00000485614.5	TSL:5	c.*79T>G		3_prime_UTR	Exon 5 of 5	ENSP00000417841.1	J3KR52

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15839 AN: 152126 Hom.: 1201 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0873

Gnomad ASJ AF: 0.0585

Gnomad EAS AF: 0.0896

Gnomad SAS AF: 0.0865

Gnomad FIN AF: 0.0605

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0560

Gnomad OTH AF: 0.0833

GnomAD2 exomes AF: 0.0796 AC: 19970 AN: 250976 AF XY: 0.0768

Gnomad AFR exome AF: 0.215

Gnomad AMR exome AF: 0.0909

Gnomad ASJ exome AF: 0.0658

Gnomad EAS exome AF: 0.101

Gnomad FIN exome AF: 0.0578

Gnomad NFE exome AF: 0.0562

Gnomad OTH exome AF: 0.0645

GnomAD4 exome AF: 0.0640 AC: 93481 AN: 1459978 Hom.: 3553 Cov.: 31 AF XY: 0.0644 AC XY: 46775 AN XY: 726110

African (AFR) AF: 0.218 AC: 7278 AN: 33394

American (AMR) AF: 0.0907 AC: 4048 AN: 44630

Ashkenazi Jewish (ASJ) AF: 0.0640 AC: 1672 AN: 26116

East Asian (EAS) AF: 0.0825 AC: 3273 AN: 39650

South Asian (SAS) AF: 0.0880 AC: 7585 AN: 86212

European-Finnish (FIN) AF: 0.0600 AC: 3204 AN: 53404

Middle Eastern (MID) AF: 0.0618 AC: 356 AN: 5760

European-Non Finnish (NFE) AF: 0.0556 AC: 61780 AN: 1110484

Other (OTH) AF: 0.0710 AC: 4285 AN: 60328

GnomAD4 genome AF: 0.104 AC: 15880 AN: 152244 Hom.: 1208 Cov.: 33 AF XY: 0.105 AC XY: 7837 AN XY: 74468

African (AFR) AF: 0.211 AC: 8778 AN: 41526

American (AMR) AF: 0.0877 AC: 1341 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0585 AC: 203 AN: 3468

East Asian (EAS) AF: 0.0897 AC: 465 AN: 5186

South Asian (SAS) AF: 0.0858 AC: 414 AN: 4826

European-Finnish (FIN) AF: 0.0605 AC: 642 AN: 10612

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0560 AC: 3810 AN: 68028

Other (OTH) AF: 0.0834 AC: 176 AN: 2110

Alfa AF: 0.0721 Hom.: 2279

Bravo AF: 0.111

Asia WGS AF: 0.104 AC: 360 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)
-	-	1	Infantile liver failure syndrome 3 (1)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		-0.28
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs864687; hg19: chr7-105205917; COSMIC: COSV57557818; COSMIC: COSV57557818;