rs6136556

Variant names:

• chr20-18889416-A-G
• rs6136556

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 0.317 in 152,036 control chromosomes in the GnomAD database, including 7,974 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 0.32 (7974 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

ACMG classification

Verdict is Benign. Variant got -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 = 0.477 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: 0.317 AC: 48196 AN: 151918 Hom.: 7977 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.296

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.317 AC: 48214 AN: 152036 Hom.: 7974 Cov.: 32 AF XY: 0.323 AC XY: 24008 AN XY: 74324

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.402

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.337

Gnomad4 OTH AF: 0.318

Alfa AF: 0.326 Hom.: 1552

Bravo AF: 0.311

Asia WGS AF: 0.451 AC: 1568 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	3.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6136556; hg19: chr20-18870060;