14-89831931-C-T

Variant names:

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

Variant summary

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

The NM_145231.4(EFCAB11):​c.411-34607G>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
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145231.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB11	NM_145231.4	MANE Select	c.411-34607G>A		intron	N/A	NP_660274.1	Q9BUY7-1
	EFCAB11	NM_001284269.2		c.339-34607G>A		intron	N/A	NP_001271198.1	Q9BUY7-2
	EFCAB11	NM_001284267.2		c.267-34607G>A		intron	N/A	NP_001271196.1	Q9BUY7-6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB11	ENST00000316738.12	TSL:2 MANE Select	c.411-34607G>A		intron	N/A	ENSP00000326267.7	Q9BUY7-1
	EFCAB11	ENST00000555872.5	TSL:1	c.339-34607G>A		intron	N/A	ENSP00000452320.1	Q9BUY7-2
	EFCAB11	ENST00000905285.1		c.536+5089G>A		intron	N/A	ENSP00000575344.1

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

African (AFR) AF: 0.905 AC: 37537 AN: 41492

American (AMR) AF: 0.859 AC: 13115 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.884 AC: 3066 AN: 3468

East Asian (EAS) AF: 0.723 AC: 3733 AN: 5166

South Asian (SAS) AF: 0.692 AC: 3327 AN: 4808

European-Finnish (FIN) AF: 0.865 AC: 9162 AN: 10586

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60879 AN: 67990

Other (OTH) AF: 0.881 AC: 1860 AN: 2112

Alfa AF: 0.886 Hom.: 146633

Bravo AF: 0.886

Asia WGS AF: 0.710 AC: 2473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.63
PhyloP100		-0.018
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: rs8021963; hg19: chr14-90298275;