rs10123149

Variant names:

• chr9-2273601-G-A
• rs10123149

Your query was ambiguous. Multiple possible variants found:

• chr9-2273601-G-A
• chr9-2273601-G-C
• chr9-2273601-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 0.503 in 152,064 control chromosomes in the GnomAD database, including 20,442 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 0.50 (20442 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.503 AC: 76448 AN: 151946 Hom.: 20421 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.503 AC: 76518 AN: 152064 Hom.: 20442 Cov.: 32 AF XY: 0.510 AC XY: 37916 AN XY: 74334

Gnomad4 AFR AF: 0.642

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.491

Alfa AF: 0.397 Hom.: 6423

Bravo AF: 0.515

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	1.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10123149; hg19: chr9-2273601;