rs9264942

chr6-31306603-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_926691.3(LOC112267902):n.964+175A>G variant causes a intron, non coding transcript 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: LOC112267902 XR_926691.3 intron, non_coding_transcript
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -1.43

Genes affected

LOC112267902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267902	XR_926691.3	n.964+175A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.580

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.367

Alfa AF: 0.369 Hom.: 19478

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

risk factor, no assertion criteria provided

literature only

OMIM

Dec 01, 2009

- -

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9264942; hg19: chr6-31274380;