Genetic Variant ENSG00000310084:n.303T>C (chr6-32473323-A-G) – 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 ENST00000846999.1(ENSG00000310084):n.303T>C 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: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ENSG00000310084
ENST00000846999.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.96

Publications

27 publications found

Variant links:

Genes affected

ENSG00000310084 (HGNC:):

ENSG00000310084 links:

HLA-DRB9 (HGNC:4957): (major histocompatibility complex, class II, DR beta 9 (pseudogene))

HLA-DRB9 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=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310084	ENST00000846999.1 link	n.303T>C		non_coding_transcript_exon_variant	Exon 1 of 1
HLA-DRB9	ENST00000449413.1 link	n.76+102T>C		intron_variant	Intron 1 of 1	6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

588176

Hom.:

AF XY:

0.00

AC XY:

AN XY:

319532

African (AFR)

AF:

0.00

AC:

AN:

14662

American (AMR)

AF:

0.00

AC:

AN:

29654

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18536

East Asian (EAS)

AF:

0.00

AC:

AN:

34556

South Asian (SAS)

AF:

0.00

AC:

AN:

60394

European-Finnish (FIN)

AF:

0.00

AC:

AN:

51428

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2450

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

345872

Other (OTH)

AF:

0.00

AC:

AN:

30624

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.14

(source)

DANN

Benign

0.34

PhyloP100

-5.0

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