rs6113161

Variant names:

• chr20-2191003-A-G
• rs6113161

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.277 in 152,152 control chromosomes in the GnomAD database, including 7,576 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 0.28 (7576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.478
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 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: 0.277 AC: 42082 AN: 152034 Hom.: 7535 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.277 AC: 42178 AN: 152152 Hom.: 7576 Cov.: 32 AF XY: 0.274 AC XY: 20381 AN XY: 74402

African (AFR) AF: 0.514 AC: 21319 AN: 41466

American (AMR) AF: 0.204 AC: 3112 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 966 AN: 3468

East Asian (EAS) AF: 0.226 AC: 1171 AN: 5182

South Asian (SAS) AF: 0.219 AC: 1057 AN: 4818

European-Finnish (FIN) AF: 0.170 AC: 1800 AN: 10604

Middle Eastern (MID) AF: 0.274 AC: 80 AN: 292

European-Non Finnish (NFE) AF: 0.176 AC: 11975 AN: 68010

Other (OTH) AF: 0.277 AC: 585 AN: 2114

Alfa AF: 0.208 Hom.: 6572

Bravo AF: 0.291

Asia WGS AF: 0.283 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.7
DANN	Benign	0.45
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs6113161; hg19: chr20-2171649;