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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.220

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10904422; hg19: chr10-5151228;