rs116979167

Variant names:

• chr7-105582004-C-A
• rs116979167
• ENST00000469099.5:c.-81+9301G>T

Your query was ambiguous. Multiple possible variants found:

• chr7-105582004-C-A
• chr7-105582004-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000469099.5(EFCAB10):​c.-81+9301G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 151,570 control chromosomes in the GnomAD database, including 1,368 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1368 hom., cov: 32)
• Consequence: EFCAB10 ENST00000469099.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.81
• Publications: 4 publications found

Genes affected

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

ENSG00000295921 (HGNC:):

YBX1P2 (HGNC:22635): (Y-box binding protein 1 pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000469099.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB10	ENST00000469099.5	TSL:3	c.-81+9301G>T		intron	N/A	ENSP00000495682.1	A0A2R8Y6P2
	EFCAB10	ENST00000490493.1	TSL:3	c.-81+9301G>T		intron	N/A	ENSP00000494437.1	A0A2R8YDC4
	ENSG00000295921	ENST00000733947.1		n.460C>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17758 AN: 151450 Hom.: 1367 Cov.: 32

Gnomad AFR AF: 0.0446

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.110

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.117 AC: 17765 AN: 151570 Hom.: 1368 Cov.: 32 AF XY: 0.119 AC XY: 8772 AN XY: 74004

African (AFR) AF: 0.0446 AC: 1840 AN: 41272

American (AMR) AF: 0.121 AC: 1843 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3470

East Asian (EAS) AF: 0.0205 AC: 106 AN: 5172

South Asian (SAS) AF: 0.224 AC: 1075 AN: 4800

European-Finnish (FIN) AF: 0.185 AC: 1937 AN: 10446

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10184 AN: 67868

Other (OTH) AF: 0.108 AC: 228 AN: 2104

Alfa AF: 0.0724 Hom.: 113

Bravo AF: 0.108

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	2.2
DANN	Benign	0.51
PhyloP100		1.8
PromoterAI		0.0087	Neutral

Splicing

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

Other links and lift over

dbSNP: rs116979167; hg19: chr7-105222451;