rs945189

Variant names:

• chr10-97332009-C-G
• rs945189

Variant summary

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

The variant allele was found at a frequency of 0.532 in 152,142 control chromosomes in the GnomAD database, including 23,193 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 0.53 (23193 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80950 AN: 152024 Hom.: 23198 Cov.: 33

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.532 AC: 80964 AN: 152142 Hom.: 23193 Cov.: 33 AF XY: 0.538 AC XY: 40000 AN XY: 74362

African (AFR) AF: 0.294 AC: 12191 AN: 41508

American (AMR) AF: 0.619 AC: 9467 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2515 AN: 3466

East Asian (EAS) AF: 0.689 AC: 3561 AN: 5172

South Asian (SAS) AF: 0.613 AC: 2960 AN: 4826

European-Finnish (FIN) AF: 0.604 AC: 6394 AN: 10588

Middle Eastern (MID) AF: 0.685 AC: 200 AN: 292

European-Non Finnish (NFE) AF: 0.614 AC: 41732 AN: 67982

Other (OTH) AF: 0.578 AC: 1220 AN: 2112

Alfa AF: 0.563 Hom.: 3124

Bravo AF: 0.524

Asia WGS AF: 0.628 AC: 2186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs945189; hg19: chr10-99091766;