10-89067022-A-G

Variant names:

• chr10-89067022-A-G
• rs1937332

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 0.463 in 151,854 control chromosomes in the GnomAD database, including 16,564 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 0.46 (16564 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 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: 0.462 AC: 70171 AN: 151736 Hom.: 16534 Cov.: 31

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.463 AC: 70249 AN: 151854 Hom.: 16564 Cov.: 31 AF XY: 0.457 AC XY: 33940 AN XY: 74202

African (AFR) AF: 0.536 AC: 22205 AN: 41440

American (AMR) AF: 0.492 AC: 7492 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1173 AN: 3460

East Asian (EAS) AF: 0.221 AC: 1141 AN: 5166

South Asian (SAS) AF: 0.374 AC: 1802 AN: 4812

European-Finnish (FIN) AF: 0.384 AC: 4058 AN: 10576

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30912 AN: 67852

Other (OTH) AF: 0.435 AC: 918 AN: 2108

Alfa AF: 0.449 Hom.: 36402

Bravo AF: 0.470

Asia WGS AF: 0.333 AC: 1159 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.48
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1937332; hg19: chr10-90826779;