14-89829353-G-T

Position:

• chr14-89829353-G-T

Variant summary

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

The NM_145231.4(EFCAB11):​c.411-32029C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 152,062 control chromosomes in the GnomAD database, including 13,631 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 0.40 (13631 hom., cov: 32)
• Consequence: EFCAB11 NM_145231.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EFCAB11	NM_145231.4	c.411-32029C>A		intron_variant		ENST00000316738.12
EFCAB11	NM_001284267.2	c.267-32029C>A		intron_variant
EFCAB11	NM_001284269.2	c.339-32029C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EFCAB11	ENST00000316738.12	c.411-32029C>A		intron_variant		2	NM_145231.4	P1

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61246 AN: 151944 Hom.: 13609 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.403 AC: 61328 AN: 152062 Hom.: 13631 Cov.: 32 AF XY: 0.407 AC XY: 30272 AN XY: 74352

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.411

Alfa AF: 0.332 Hom.: 14993

Bravo AF: 0.423

Asia WGS AF: 0.577 AC: 2006 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	11
DANN	Benign	0.74

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: rs8005836; hg19: chr14-90295697;