chr14-89831931-C-T

Variant names:

• chr14-89831931-C-T
• rs8021963
• NM_145231.4:c.411-34607G>A

Variant summary

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

The NM_145231.4(EFCAB11):​c.411-34607G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,098 control chromosomes in the GnomAD database, including 59,020 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 0.88 (59020 hom., cov: 30)
• Consequence: EFCAB11 NM_145231.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB11	NM_145231.4	c.411-34607G>A		intron_variant	Intron 5 of 5	ENST00000316738.12	NP_660274.1
EFCAB11	NM_001284269.2	c.339-34607G>A		intron_variant	Intron 5 of 5		NP_001271198.1
EFCAB11	NM_001284267.2	c.267-34607G>A		intron_variant	Intron 5 of 5		NP_001271196.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFCAB11	ENST00000316738.12	c.411-34607G>A		intron_variant	Intron 5 of 5	2	NM_145231.4	ENSP00000326267.7

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133689 AN: 151982 Hom.: 58976 Cov.: 30

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.884

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.880 AC: 133791 AN: 152098 Hom.: 59020 Cov.: 30 AF XY: 0.873 AC XY: 64886 AN XY: 74350

Gnomad4 AFR AF: 0.905

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.884

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.881

Alfa AF: 0.881 Hom.: 40638

Bravo AF: 0.886

Asia WGS AF: 0.710 AC: 2473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.63

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: rs8021963; hg19: chr14-90298275;