rs116979167

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFCAB10	ENST00000469099.5	c.-81+9301G>T		intron_variant		3		ENSP00000495682
EFCAB10	ENST00000490493.1	c.-81+9301G>T		intron_variant		3		ENSP00000494437

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

Gnomad4 AFR AF: 0.0446

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0205

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0724 Hom.: 113

Bravo AF: 0.108

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	2.2
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs116979167; hg19: chr7-105222451;