rs10904422

Variant names:

• chr10-5109036-G-C
• rs10904422

Your query was ambiguous. Multiple possible variants found:

• chr10-5109036-G-C
• chr10-5109036-G-T

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 0.191 in 152,032 control chromosomes in the GnomAD database, including 3,704 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 0.19 (3704 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 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: 0.191 AC: 29074 AN: 151912 Hom.: 3705 Cov.: 32

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.191 AC: 29083 AN: 152032 Hom.: 3704 Cov.: 32 AF XY: 0.197 AC XY: 14611 AN XY: 74300

African (AFR) AF: 0.135 AC: 5589 AN: 41464

American (AMR) AF: 0.264 AC: 4030 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1151 AN: 3466

East Asian (EAS) AF: 0.626 AC: 3233 AN: 5166

South Asian (SAS) AF: 0.441 AC: 2122 AN: 4814

European-Finnish (FIN) AF: 0.107 AC: 1126 AN: 10560

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11170 AN: 67986

Other (OTH) AF: 0.220 AC: 464 AN: 2110

Alfa AF: 0.0511 Hom.: 58

Bravo AF: 0.200

Asia WGS AF: 0.484 AC: 1683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.69
DANN	Benign	0.40
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10904422; hg19: chr10-5151228;