chr1-46713638-A-G

Position:

• chr1-46713638-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014774.3(EFCAB14):​c.334+2657T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,082 control chromosomes in the GnomAD database, including 49,397 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 0.80 (49397 hom., cov: 31)
• Consequence: EFCAB14 NM_014774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00

Genes affected

EFCAB14 (HGNC:29051): (EF-hand calcium binding domain 14) Predicted to enable calcium ion binding activity. Predicted to be integral component of membrane. [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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.89 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EFCAB14	NM_014774.3	c.334+2657T>C		intron_variant		ENST00000371933.8	NP_055589.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFCAB14	ENST00000371933.8	c.334+2657T>C		intron_variant		1	NM_014774.3	ENSP00000361001	P2

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122237 AN: 151964 Hom.: 49325 Cov.: 31

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.912

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.805 AC: 122365 AN: 152082 Hom.: 49397 Cov.: 31 AF XY: 0.807 AC XY: 60003 AN XY: 74342

Gnomad4 AFR AF: 0.837

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.912

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.827

Alfa AF: 0.780 Hom.: 45411

Bravo AF: 0.814

Asia WGS AF: 0.822 AC: 2858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	7.0
DANN	Benign	0.33

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

Publications

LitVar

Other links and lift over

dbSNP: rs10789491; hg19: chr1-47179310;