14-89839316-A-G

Variant names:

• chr14-89839316-A-G
• rs4900016
• NM_145231.4:c.411-41992T>C

Variant summary

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

The NM_145231.4(EFCAB11):​c.411-41992T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.735 in 152,056 control chromosomes in the GnomAD database, including 42,615 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 0.73 (42615 hom., cov: 31)
• Consequence: EFCAB11 NM_145231.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB11	NM_145231.4	c.411-41992T>C		intron_variant	Intron 5 of 5	ENST00000316738.12	NP_660274.1
EFCAB11	NM_001284269.2	c.339-41992T>C		intron_variant	Intron 5 of 5		NP_001271198.1
EFCAB11	NM_001284267.2	c.267-41992T>C		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.411-41992T>C		intron_variant	Intron 5 of 5	2	NM_145231.4	ENSP00000326267.7

Frequencies

GnomAD3 genomes AF: 0.735 AC: 111662 AN: 151940 Hom.: 42610 Cov.: 31

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.793

Gnomad NFE AF: 0.854

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.735 AC: 111707 AN: 152056 Hom.: 42615 Cov.: 31 AF XY: 0.731 AC XY: 54330 AN XY: 74320

African (AFR) AF: 0.518 AC: 21477 AN: 41424

American (AMR) AF: 0.771 AC: 11778 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2752 AN: 3472

East Asian (EAS) AF: 0.619 AC: 3208 AN: 5182

South Asian (SAS) AF: 0.662 AC: 3185 AN: 4810

European-Finnish (FIN) AF: 0.816 AC: 8634 AN: 10578

Middle Eastern (MID) AF: 0.808 AC: 236 AN: 292

European-Non Finnish (NFE) AF: 0.854 AC: 58056 AN: 67998

Other (OTH) AF: 0.754 AC: 1587 AN: 2106

Alfa AF: 0.812 Hom.: 26228

Bravo AF: 0.725

Asia WGS AF: 0.611 AC: 2127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.67
PhyloP100		-1.2
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: rs4900016; hg19: chr14-90305660;