rs7147996

chr14-89930230-T-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
EFCAB11	NM_145231.4	c.410+1311A>T		intron_variant		ENST00000316738.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFCAB11	ENST00000316738.12	c.410+1311A>T		intron_variant		2	NM_145231.4	P1

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

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.347

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

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: rs7147996; hg19: chr14-90396574;