rs9290105

Positions:

• chr3-161957236-A-G

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 0.0852 in 152,128 control chromosomes in the GnomAD database, including 782 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 0.085 (782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.129 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: 0.0853 AC: 12961 AN: 152010 Hom.: 783 Cov.: 32

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0515

Gnomad ASJ AF: 0.0453

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.0672

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0852 AC: 12958 AN: 152128 Hom.: 782 Cov.: 32 AF XY: 0.0847 AC XY: 6303 AN XY: 74378

Gnomad4 AFR AF: 0.0234

Gnomad4 AMR AF: 0.0515

Gnomad4 ASJ AF: 0.0453

Gnomad4 EAS AF: 0.00578

Gnomad4 SAS AF: 0.0674

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.113 Hom.: 140

Bravo AF: 0.0726

Asia WGS AF: 0.0330 AC: 115 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9290105; hg19: chr3-161675024;