Genetic Variant AKR1C6P:n.516C>A (chr10-4885460-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000432950.1(AKR1C6P):n.516C>A variant causes a non coding transcript exon 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: 30)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

AKR1C6P
ENST00000432950.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.166

Publications

4 publications found

Variant links:

Genes affected

AKR1C6P (HGNC:44680): (aldo-keto reductase family 1 member C6, pseudogene)

AKR1C6P links:

ENSG00000304775 (HGNC:):

ENSG00000304775 links:

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ACMG classification

Classification was made for transcript

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=-0.59).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKR1C6P	NR_026743.1 link	n.653-367C>A		intron_variant	Intron 6 of 10

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
AKR1C6P	ENST00000432950.1 link	n.516C>A	non_coding_transcript_exon_variant	Exon 5 of 9	6
ENSG00000304775	ENST00000806213.1 link	n.662+1878C>A	intron_variant	Intron 5 of 8
ENSG00000304775	ENST00000806214.1 link	n.135-7896C>A	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

604822

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

330438

African (AFR)

AF:

0.00

AC:

AN:

17162

American (AMR)

AF:

0.00

AC:

AN:

42862

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19978

East Asian (EAS)

AF:

0.00

AC:

AN:

35320

South Asian (SAS)

AF:

0.00

AC:

AN:

69340

European-Finnish (FIN)

AF:

0.00

AC:

AN:

49960

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3078

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

335962

Other (OTH)

AF:

0.00

AC:

AN:

31160

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

2.4

(source)

DANN

Benign

0.81

PhyloP100

0.17

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over