rs10511894

Variant names:

• chr9-32082271-T-C
• rs10511894
• ENST00000835650.1:n.326-29899T>C

Variant summary

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

The ENST00000835650.1(ENSG00000308674):​n.326-29899T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 152,076 control chromosomes in the GnomAD database, including 5,943 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 0.27 (5943 hom., cov: 33)
• Consequence: ENSG00000308674 ENST00000835650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 0 publications found

Genes affected

ENSG00000308674 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835650.1. 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
	ENSG00000308674	ENST00000835650.1		n.326-29899T>C		intron	N/A
	ENSG00000308674	ENST00000835651.1		n.435-3083T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41126 AN: 151958 Hom.: 5936 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.271 AC: 41146 AN: 152076 Hom.: 5943 Cov.: 33 AF XY: 0.273 AC XY: 20274 AN XY: 74348

African (AFR) AF: 0.335 AC: 13904 AN: 41452

American (AMR) AF: 0.310 AC: 4736 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 788 AN: 3468

East Asian (EAS) AF: 0.418 AC: 2158 AN: 5162

South Asian (SAS) AF: 0.323 AC: 1557 AN: 4818

European-Finnish (FIN) AF: 0.210 AC: 2229 AN: 10598

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14877 AN: 67980

Other (OTH) AF: 0.296 AC: 625 AN: 2108

Alfa AF: 0.242 Hom.: 599

Bravo AF: 0.281

Asia WGS AF: 0.393 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.84
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs10511894; hg19: chr9-32082269;