20-6596138-G-C

Variant names:

• chr20-6596138-G-C
• rs958435

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 0.669 in 152,130 control chromosomes in the GnomAD database, including 34,370 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 0.67 (34370 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 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: 0.669 AC: 101656 AN: 152012 Hom.: 34324 Cov.: 33

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.669 AC: 101754 AN: 152130 Hom.: 34370 Cov.: 33 AF XY: 0.671 AC XY: 49912 AN XY: 74370

African (AFR) AF: 0.656 AC: 27245 AN: 41510

American (AMR) AF: 0.770 AC: 11762 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1960 AN: 3468

East Asian (EAS) AF: 0.820 AC: 4244 AN: 5178

South Asian (SAS) AF: 0.566 AC: 2727 AN: 4820

European-Finnish (FIN) AF: 0.694 AC: 7331 AN: 10570

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44187 AN: 67988

Other (OTH) AF: 0.673 AC: 1419 AN: 2108

Alfa AF: 0.661 Hom.: 4148

Bravo AF: 0.677

Asia WGS AF: 0.677 AC: 2357 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.60
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs958435; hg19: chr20-6576785;