rs7147996

Variant names:

• chr14-89930230-T-A
• rs7147996
• NM_145231.4:c.410+1311A>T

Variant summary

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

The NM_145231.4(EFCAB11):​c.410+1311A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,182 control chromosomes in the GnomAD database, including 10,793 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 0.34 (10793 hom., cov: 33)
• Consequence: EFCAB11 NM_145231.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.213
• Publications: 7 publications found

Genes affected

EFCAB11 (HGNC:20357): (EF-hand calcium binding domain 11) Predicted to enable calcium ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000259053 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB11	NM_145231.4	c.410+1311A>T		intron_variant	Intron 5 of 5	ENST00000316738.12	NP_660274.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFCAB11	ENST00000316738.12	c.410+1311A>T		intron_variant	Intron 5 of 5	2	NM_145231.4	ENSP00000326267.7

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52361 AN: 152064 Hom.: 10796 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.344 AC: 52359 AN: 152182 Hom.: 10793 Cov.: 33 AF XY: 0.345 AC XY: 25648 AN XY: 74392

African (AFR) AF: 0.127 AC: 5283 AN: 41532

American (AMR) AF: 0.284 AC: 4344 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1601 AN: 3470

East Asian (EAS) AF: 0.185 AC: 955 AN: 5176

South Asian (SAS) AF: 0.402 AC: 1940 AN: 4820

European-Finnish (FIN) AF: 0.497 AC: 5259 AN: 10588

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31568 AN: 67996

Other (OTH) AF: 0.347 AC: 733 AN: 2110

Alfa AF: 0.403 Hom.: 1689

Bravo AF: 0.318

Asia WGS AF: 0.288 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.7
DANN	Benign	0.76
PhyloP100		0.21
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: rs7147996; hg19: chr14-90396574;