NM_014774.3:c.1313-2100A>G

Variant names:

• chr1-46680736-T-C
• rs12048954
• NM_014774.3:c.1313-2100A>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.1313-2100A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 152,128 control chromosomes in the GnomAD database, including 12,269 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 0.37 (12269 hom., cov: 32)
• Consequence: EFCAB14 NM_014774.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 4 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]

EFCAB14-AS1 (HGNC:44108): (EFCAB14 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB14	NM_014774.3	c.1313-2100A>G		intron_variant	Intron 10 of 10	ENST00000371933.8	NP_055589.1
EFCAB14-AS1	NR_038827.1	n.185-1445T>C		intron_variant	Intron 1 of 3
EFCAB14-AS1	NR_038828.1	n.185-5937T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFCAB14	ENST00000371933.8	c.1313-2100A>G		intron_variant	Intron 10 of 10	1	NM_014774.3	ENSP00000361001.3

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55574 AN: 152010 Hom.: 12272 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.365 AC: 55562 AN: 152128 Hom.: 12269 Cov.: 32 AF XY: 0.362 AC XY: 26940 AN XY: 74364

African (AFR) AF: 0.122 AC: 5083 AN: 41520

American (AMR) AF: 0.403 AC: 6159 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1436 AN: 3470

East Asian (EAS) AF: 0.133 AC: 690 AN: 5186

South Asian (SAS) AF: 0.320 AC: 1542 AN: 4824

European-Finnish (FIN) AF: 0.480 AC: 5066 AN: 10558

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.503 AC: 34187 AN: 67974

Other (OTH) AF: 0.387 AC: 814 AN: 2106

Alfa AF: 0.407 Hom.: 2266

Bravo AF: 0.350

Asia WGS AF: 0.205 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.3
DANN	Benign	0.84
PhyloP100		-0.44
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: rs12048954; hg19: chr1-47146408;