rs2161

Positions:

• chr7-98463194-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.367 in 151,998 control chromosomes in the GnomAD database, including 10,771 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 0.37 (10771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.548 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: 0.367 AC: 55681 AN: 151880 Hom.: 10755 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.367 AC: 55738 AN: 151998 Hom.: 10771 Cov.: 32 AF XY: 0.372 AC XY: 27615 AN XY: 74286

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.565

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.333

Alfa AF: 0.304 Hom.: 14850

Bravo AF: 0.370

Asia WGS AF: 0.450 AC: 1568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	18
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2161; hg19: chr7-98092506; COSMIC: COSV62496727;