rs2181038

chr9-101861161-A-Cchr9-101861161-A-Gchr9-101861161-A-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 0.751 in 152,114 control chromosomes in the GnomAD database, including 43,094 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 0.75 (43094 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 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: 0.751 AC: 114177 AN: 151996 Hom.: 43051 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.804

Gnomad AMR AF: 0.768

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.764

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

GnomAD4 genome AF: 0.751 AC: 114276 AN: 152114 Hom.: 43094 Cov.: 32 AF XY: 0.746 AC XY: 55489 AN XY: 74350

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.768

Gnomad4 ASJ AF: 0.749

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.759

Alfa AF: 0.739 Hom.: 53884

Bravo AF: 0.770

Asia WGS AF: 0.764 AC: 2661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.038
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2181038; hg19: chr9-104623443;