rs6101183

Variant names:

• chr20-61016904-C-T
• rs6101183

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 0.492 in 151,914 control chromosomes in the GnomAD database, including 18,423 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 0.49 (18423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.597 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: 0.492 AC: 74732 AN: 151796 Hom.: 18411 Cov.: 32

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.495

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.492 AC: 74798 AN: 151914 Hom.: 18423 Cov.: 32 AF XY: 0.496 AC XY: 36827 AN XY: 74268

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.616

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.495

Gnomad4 OTH AF: 0.511

Alfa AF: 0.503 Hom.: 10351

Bravo AF: 0.495

Asia WGS AF: 0.558 AC: 1939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.022
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6101183; hg19: chr20-59591960;