rs1048380

chr1-46676866-G-A

Variant summary

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

The NM_014774.3(EFCAB14):c.*1595C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,730 control chromosomes in the GnomAD database, including 4,819 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 0.24 (4808 hom., cov: 31)
  • Exomes 𝑓: 0.25 (11 hom.)
• Consequence: EFCAB14 NM_014774.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFCAB14	NM_014774.3	c.*1595C>T		3_prime_UTR_variant	11/11	ENST00000371933.8
EFCAB14-AS1	NR_038827.1	n.184+2647G>A		intron_variant, non_coding_transcript_variant
EFCAB14-AS1	NR_038828.1	n.184+2647G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFCAB14	ENST00000371933.8	c.*1595C>T		3_prime_UTR_variant	11/11	1	NM_014774.3	P2
EFCAB14-AS1	ENST00000442839.5	n.184+2647G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36810 AN: 151182 Hom.: 4800 Cov.: 31

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.286

GnomAD4 exome AF: 0.252 AC: 108 AN: 428 Hom.: 11 Cov.: 0 AF XY: 0.236 AC XY: 61 AN XY: 258

Gnomad4 FIN exome AF: 0.254

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.244 AC: 36844 AN: 151302 Hom.: 4808 Cov.: 31 AF XY: 0.247 AC XY: 18250 AN XY: 73892

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.287

Alfa AF: 0.259 Hom.: 8063

Bravo AF: 0.246

Asia WGS AF: 0.269 AC: 936 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	2.7
Dann	Benign	0.68

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: rs1048380; hg19: chr1-47142538;