22-43642638-G-A

Position:

• chr22-43642638-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
EFCAB6	NM_022785.4	c.1984-7422C>T		intron_variant		ENST00000262726.12	NP_073622.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EFCAB6	ENST00000262726.12	c.1984-7422C>T		intron_variant		2	NM_022785.4	ENSP00000262726	P1
EFCAB6	ENST00000396231.6	c.1528-7422C>T		intron_variant		1		ENSP00000379533
EFCAB6	ENST00000468552.1	n.530-7422C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.769

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.607

Gnomad4 NFE AF: 0.529

Gnomad4 OTH AF: 0.567

Alfa AF: 0.538 Hom.: 6564

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

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: rs713912; hg19: chr22-44038518;