rs2071716

Variant names:

• chr22-43683558-A-C
• rs2071716
• NM_022785.4:c.1251+189T>G

Your query was ambiguous. Multiple possible variants found:

• chr22-43683558-A-C
• chr22-43683558-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_022785.4(EFCAB6):​c.1251+189T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: EFCAB6 NM_022785.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022785.4. 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
	EFCAB6	NM_022785.4	MANE Select	c.1251+189T>G		intron	N/A	NP_073622.2
	EFCAB6	NM_198856.3		c.795+189T>G		intron	N/A	NP_942153.1	Q5THR3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EFCAB6	ENST00000262726.12	TSL:2 MANE Select	c.1251+189T>G		intron	N/A	ENSP00000262726.7	Q5THR3-1
	EFCAB6	ENST00000396231.6	TSL:1	c.795+189T>G		intron	N/A	ENSP00000379533.2	Q5THR3-2
	EFCAB6	ENST00000970826.1		c.1251+189T>G		intron	N/A	ENSP00000640885.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 420634 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 220620

African (AFR) AF: 0.00 AC: 0 AN: 12068

American (AMR) AF: 0.00 AC: 0 AN: 17832

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12974

East Asian (EAS) AF: 0.00 AC: 0 AN: 30398

South Asian (SAS) AF: 0.00 AC: 0 AN: 38506

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29620

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1858

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 252884

Other (OTH) AF: 0.00 AC: 0 AN: 24494

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1778

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.1
DANN	Benign	0.70
PhyloP100		1.3

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: rs2071716; hg19: chr22-44079438;