10-22741353-G-A

Variant names:

• chr10-22741353-G-A
• rs7091875
• ENST00000756996.1:n.497-8308C>T

Variant summary

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

The ENST00000756996.1(ENSG00000298626):​n.497-8308C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,838 control chromosomes in the GnomAD database, including 10,658 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 0.36 (10658 hom., cov: 31)
• Consequence: ENSG00000298626 ENST00000756996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 2 publications found

Genes affected

ENSG00000298626 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756996.1. 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
	ENSG00000298626	ENST00000756996.1		n.497-8308C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54333 AN: 151720 Hom.: 10647 Cov.: 31

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.358 AC: 54381 AN: 151838 Hom.: 10658 Cov.: 31 AF XY: 0.350 AC XY: 25986 AN XY: 74176

African (AFR) AF: 0.518 AC: 21402 AN: 41350

American (AMR) AF: 0.268 AC: 4089 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1213 AN: 3468

East Asian (EAS) AF: 0.151 AC: 783 AN: 5170

South Asian (SAS) AF: 0.365 AC: 1755 AN: 4812

European-Finnish (FIN) AF: 0.222 AC: 2330 AN: 10514

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.319 AC: 21656 AN: 67956

Other (OTH) AF: 0.376 AC: 792 AN: 2108

Alfa AF: 0.332 Hom.: 21708

Bravo AF: 0.366

Asia WGS AF: 0.265 AC: 921 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.31
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs7091875; hg19: chr10-23030282;