rs12048954

chr1-46680736-T-Cchr1-46680736-T-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
EFCAB14	NM_014774.3	c.1313-2100A>G		intron_variant		ENST00000371933.8
EFCAB14-AS1	NR_038827.1	n.185-1445T>C		intron_variant, non_coding_transcript_variant
EFCAB14-AS1	NR_038828.1	n.185-5937T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFCAB14	ENST00000371933.8	c.1313-2100A>G		intron_variant		1	NM_014774.3	P2
EFCAB14-AS1	ENST00000442839.5	n.185-5937T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.133

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.387

Alfa AF: 0.415 Hom.: 2253

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

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: rs12048954; hg19: chr1-47146408;