rs713912

Variant names:

• chr22-43642638-G-A
• rs713912
• NM_022785.4:c.1984-7422C>T

Your query was ambiguous. Multiple possible variants found:

• chr22-43642638-G-A
• chr22-43642638-G-T

Variant summary

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

The NM_022785.4(EFCAB6):​c.1984-7422C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,026 control chromosomes in the GnomAD database, including 23,439 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 0.55 (23439 hom., cov: 32)
• Consequence: EFCAB6 NM_022785.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 4 publications found

Genes affected

EFCAB6 (HGNC:24204): (EF-hand calcium binding domain 6) This gene encodes a protein which directly binds the oncogene DJ-1 and androgen receptor to form a ternary complex in cells. This binding protein recruits histone-deacetylase complexes in order to repress transcription activity of androgen receptor. This protein may also play a role in spermatogenesis and fertilization. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EFCAB6	NM_022785.4	c.1984-7422C>T		intron_variant	Intron 17 of 31	ENST00000262726.12	NP_073622.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EFCAB6	ENST00000262726.12	c.1984-7422C>T		intron_variant	Intron 17 of 31	2	NM_022785.4	ENSP00000262726.7
EFCAB6	ENST00000396231.6	c.1528-7422C>T		intron_variant	Intron 15 of 29	1		ENSP00000379533.2
EFCAB6	ENST00000468552.1	n.530-7422C>T		intron_variant	Intron 4 of 12	1

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83775 AN: 151908 Hom.: 23403 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.607

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.552 AC: 83866 AN: 152026 Hom.: 23439 Cov.: 32 AF XY: 0.556 AC XY: 41308 AN XY: 74314

African (AFR) AF: 0.510 AC: 21159 AN: 41450

American (AMR) AF: 0.646 AC: 9861 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3470

East Asian (EAS) AF: 0.769 AC: 3976 AN: 5168

South Asian (SAS) AF: 0.540 AC: 2601 AN: 4818

European-Finnish (FIN) AF: 0.607 AC: 6418 AN: 10576

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35971 AN: 67952

Other (OTH) AF: 0.567 AC: 1197 AN: 2112

Alfa AF: 0.537 Hom.: 6653

Bravo AF: 0.558

Asia WGS AF: 0.631 AC: 2195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.73
PhyloP100		0.10
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: rs713912; hg19: chr22-44038518;