chr10-9011169-C-T

Variant names:

• chr10-9011169-C-T
• rs962993
• ENST00000798219.1:n.260+7528G>A

Variant summary

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

The ENST00000798219.1(ENSG00000303941):​n.260+7528G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,752 control chromosomes in the GnomAD database, including 9,189 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 0.33 (9189 hom., cov: 31)
• Consequence: ENSG00000303941 ENST00000798219.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.314
• Publications: 27 publications found

Genes affected

ENSG00000303941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000798219.1. 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
	ENSG00000303941	ENST00000798219.1		n.260+7528G>A		intron	N/A
	ENSG00000303941	ENST00000798220.1		n.329+7528G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50711 AN: 151632 Hom.: 9190 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.334 AC: 50714 AN: 151752 Hom.: 9189 Cov.: 31 AF XY: 0.326 AC XY: 24154 AN XY: 74144

African (AFR) AF: 0.235 AC: 9704 AN: 41340

American (AMR) AF: 0.311 AC: 4735 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1839 AN: 3472

East Asian (EAS) AF: 0.115 AC: 594 AN: 5146

South Asian (SAS) AF: 0.330 AC: 1584 AN: 4804

European-Finnish (FIN) AF: 0.285 AC: 2992 AN: 10504

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.412 AC: 27977 AN: 67926

Other (OTH) AF: 0.374 AC: 788 AN: 2108

Alfa AF: 0.367 Hom.: 8230

Bravo AF: 0.331

Asia WGS AF: 0.233 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.37
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs962993; hg19: chr10-9053132;