14-89822627-T-C

Variant names:

• chr14-89822627-T-C
• rs1952774
• NM_145231.4:c.411-25303A>G

Variant summary

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

The NM_145231.4(EFCAB11):​c.411-25303A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,962 control chromosomes in the GnomAD database, including 13,768 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 0.41 (13768 hom., cov: 31)
• Consequence: EFCAB11 NM_145231.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300
• Publications: 3 publications found

Genes affected

EFCAB11 (HGNC:20357): (EF-hand calcium binding domain 11) Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000259053 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145231.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB11	NM_145231.4	MANE Select	c.411-25303A>G		intron	N/A	NP_660274.1
	EFCAB11	NM_001284269.2		c.339-25303A>G		intron	N/A	NP_001271198.1
	EFCAB11	NM_001284267.2		c.267-25303A>G		intron	N/A	NP_001271196.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB11	ENST00000316738.12	TSL:2 MANE Select	c.411-25303A>G		intron	N/A	ENSP00000326267.7
	EFCAB11	ENST00000555872.5	TSL:1	c.339-25303A>G		intron	N/A	ENSP00000452320.1
	EFCAB11	ENST00000556609.5	TSL:3	c.267-25303A>G		intron	N/A	ENSP00000452335.1

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61490 AN: 151844 Hom.: 13746 Cov.: 31

Gnomad AFR AF: 0.562

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.405 AC: 61569 AN: 151962 Hom.: 13768 Cov.: 31 AF XY: 0.408 AC XY: 30338 AN XY: 74276

African (AFR) AF: 0.562 AC: 23278 AN: 41422

American (AMR) AF: 0.418 AC: 6375 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1570 AN: 3466

East Asian (EAS) AF: 0.715 AC: 3683 AN: 5152

South Asian (SAS) AF: 0.458 AC: 2202 AN: 4810

European-Finnish (FIN) AF: 0.272 AC: 2875 AN: 10576

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20241 AN: 67958

Other (OTH) AF: 0.414 AC: 874 AN: 2112

Alfa AF: 0.332 Hom.: 5255

Bravo AF: 0.425

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.67
PhyloP100		-0.30
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs1952774; hg19: chr14-90288971;