rs6136489

Variant names:

• chr20-1943088-T-G
• rs6136489

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 0.464 in 152,018 control chromosomes in the GnomAD database, including 18,466 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 0.46 (18466 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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: 0.463 AC: 70378 AN: 151900 Hom.: 18411 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.464 AC: 70498 AN: 152018 Hom.: 18466 Cov.: 32 AF XY: 0.465 AC XY: 34565 AN XY: 74298

African (AFR) AF: 0.681 AC: 28239 AN: 41452

American (AMR) AF: 0.432 AC: 6600 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1383 AN: 3470

East Asian (EAS) AF: 0.754 AC: 3888 AN: 5156

South Asian (SAS) AF: 0.596 AC: 2861 AN: 4800

European-Finnish (FIN) AF: 0.275 AC: 2906 AN: 10576

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22934 AN: 67960

Other (OTH) AF: 0.470 AC: 992 AN: 2110

Alfa AF: 0.383 Hom.: 51536

Bravo AF: 0.486

Asia WGS AF: 0.712 AC: 2479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.12
DANN	Benign	0.50
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6136489; hg19: chr20-1923734;