rs10123149

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;