chr1-46698934-A-C

Variant names:

• chr1-46698934-A-C
• rs6671124
• NM_014774.3:c.481-2285T>G

Variant summary

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

The NM_014774.3(EFCAB14):​c.481-2285T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,728 control chromosomes in the GnomAD database, including 15,579 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 0.42 (15579 hom., cov: 30)
• Consequence: EFCAB14 NM_014774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63
• Publications: 8 publications found

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]

ENSG00000295128 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB14	NM_014774.3	c.481-2285T>G		intron_variant	Intron 3 of 10	ENST00000371933.8	NP_055589.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFCAB14	ENST00000371933.8	c.481-2285T>G		intron_variant	Intron 3 of 10	1	NM_014774.3	ENSP00000361001.3

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63083 AN: 151610 Hom.: 15513 Cov.: 30

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.417 AC: 63215 AN: 151728 Hom.: 15579 Cov.: 30 AF XY: 0.421 AC XY: 31208 AN XY: 74148

African (AFR) AF: 0.648 AC: 26793 AN: 41318

American (AMR) AF: 0.459 AC: 6989 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1262 AN: 3460

East Asian (EAS) AF: 0.776 AC: 3963 AN: 5110

South Asian (SAS) AF: 0.409 AC: 1970 AN: 4816

European-Finnish (FIN) AF: 0.258 AC: 2723 AN: 10546

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18285 AN: 67942

Other (OTH) AF: 0.427 AC: 899 AN: 2104

Alfa AF: 0.366 Hom.: 2162

Bravo AF: 0.442

Asia WGS AF: 0.605 AC: 2102 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	0.58
DANN	Benign	0.38
PhyloP100		-1.6
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: rs6671124; hg19: chr1-47164606;