rs6113161

Variant names:

• chr20-2191003-A-G
• rs6113161

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 0.277 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.277

Alfa AF: 0.198 Hom.: 4420

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6113161; hg19: chr20-2171649;