rs9263844

Variant names:

• chr6-31187409-C-T
• rs9263844
• ENST00000755443.1:n.183-1139G>A

Variant summary

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

The ENST00000755443.1(ENSG00000272501):​n.183-1139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 151,492 control chromosomes in the GnomAD database, including 2,351 homozygotes. 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: 𝑓 0.17 (2351 hom., cov: 30)
• Consequence: ENSG00000272501 ENST00000755443.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 11 publications found

Genes affected

ENSG00000272501 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755443.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000272501	ENST00000755443.1		n.183-1139G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.165 AC: 24991 AN: 151376 Hom.: 2350 Cov.: 30

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.165 AC: 25010 AN: 151492 Hom.: 2351 Cov.: 30 AF XY: 0.170 AC XY: 12607 AN XY: 73966

African (AFR) AF: 0.120 AC: 4944 AN: 41288

American (AMR) AF: 0.214 AC: 3261 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1337 AN: 3468

East Asian (EAS) AF: 0.123 AC: 628 AN: 5126

South Asian (SAS) AF: 0.223 AC: 1068 AN: 4790

European-Finnish (FIN) AF: 0.226 AC: 2363 AN: 10434

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10642 AN: 67866

Other (OTH) AF: 0.230 AC: 482 AN: 2100

Alfa AF: 0.176 Hom.: 1094

Bravo AF: 0.164

Asia WGS AF: 0.186 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.7
DANN	Benign	0.45
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs9263844; hg19: chr6-31155186;