rs6101183

Variant names:

• chr20-61016904-C-T
• rs6101183

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 0.492 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.453 AC: 18738 AN: 41370

American (AMR) AF: 0.536 AC: 8182 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1955 AN: 3470

East Asian (EAS) AF: 0.525 AC: 2711 AN: 5162

South Asian (SAS) AF: 0.616 AC: 2967 AN: 4818

European-Finnish (FIN) AF: 0.480 AC: 5066 AN: 10560

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.495 AC: 33640 AN: 67956

Other (OTH) AF: 0.511 AC: 1076 AN: 2104

Alfa AF: 0.503 Hom.: 11307

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6101183; hg19: chr20-59591960;