20-61190239-C-T

Variant names:

• chr20-61190239-C-T
• rs860148

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 152,064 control chromosomes in the GnomAD database, including 19,621 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 (19621 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.960
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.675 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: 0.491 AC: 74667 AN: 151946 Hom.: 19589 Cov.: 33

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.492 AC: 74757 AN: 152064 Hom.: 19621 Cov.: 33 AF XY: 0.492 AC XY: 36546 AN XY: 74322

African (AFR) AF: 0.643 AC: 26674 AN: 41488

American (AMR) AF: 0.558 AC: 8531 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1549 AN: 3468

East Asian (EAS) AF: 0.694 AC: 3590 AN: 5170

South Asian (SAS) AF: 0.402 AC: 1934 AN: 4810

European-Finnish (FIN) AF: 0.382 AC: 4036 AN: 10554

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26914 AN: 67978

Other (OTH) AF: 0.496 AC: 1045 AN: 2108

Alfa AF: 0.464 Hom.: 6834

Bravo AF: 0.518

Asia WGS AF: 0.559 AC: 1947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.28
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs860148; hg19: chr20-59765295;