rs1440487

chr1-46701403-A-Gchr1-46701403-A-T

Variant summary

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

The NM_014774.3(EFCAB14):c.481-4754T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,104 control chromosomes in the GnomAD database, including 49,269 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 (49269 hom., cov: 32)
• Consequence: EFCAB14 NM_014774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFCAB14	NM_014774.3	c.481-4754T>C		intron_variant		ENST00000371933.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFCAB14	ENST00000371933.8	c.481-4754T>C		intron_variant		1	NM_014774.3	P2

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122097 AN: 151986 Hom.: 49197 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.868

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.804 AC: 122226 AN: 152104 Hom.: 49269 Cov.: 32 AF XY: 0.806 AC XY: 59950 AN XY: 74360

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.868

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.826

Alfa AF: 0.778 Hom.: 26216

Bravo AF: 0.812

Asia WGS AF: 0.821 AC: 2857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	7.3
Dann	Benign	0.79

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: rs1440487; hg19: chr1-47167075;