6-31306603-T-C

Variant names:

• chr6-31306603-T-C
• rs9264942
• ENST00000755297.1:n.32+35497T>C

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+35497T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 152,040 control chromosomes in the GnomAD database, including 9,279 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.34 (9279 hom., cov: 32)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -1.43
• Publications: 195 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755297.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298396	ENST00000755297.1		n.32+35497T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52288 AN: 151922 Hom.: 9281 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.344 AC: 52309 AN: 152040 Hom.: 9279 Cov.: 32 AF XY: 0.343 AC XY: 25522 AN XY: 74318

African (AFR) AF: 0.303 AC: 12572 AN: 41438

American (AMR) AF: 0.310 AC: 4739 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2014 AN: 3470

East Asian (EAS) AF: 0.394 AC: 2032 AN: 5158

South Asian (SAS) AF: 0.508 AC: 2450 AN: 4824

European-Finnish (FIN) AF: 0.271 AC: 2870 AN: 10586

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24370 AN: 67952

Other (OTH) AF: 0.367 AC: 775 AN: 2114

Alfa AF: 0.356 Hom.: 42381

Bravo AF: 0.344

Asia WGS AF: 0.420 AC: 1461 AN: 3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

HIV-1 VIREMIA, SUSCEPTIBILITY TO Other:1

Dec 01, 2009

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.4
DANN	Benign	0.71
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9264942; hg19: chr6-31274380;