rs6123609

Variant names:

• chr20-38343178-G-C
• rs6123609

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 0.376 in 152,064 control chromosomes in the GnomAD database, including 10,878 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 0.38 (10878 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.687
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 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: 0.376 AC: 57091 AN: 151946 Hom.: 10859 Cov.: 33

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.376 AC: 57155 AN: 152064 Hom.: 10878 Cov.: 33 AF XY: 0.378 AC XY: 28071 AN XY: 74310

African (AFR) AF: 0.389 AC: 16125 AN: 41486

American (AMR) AF: 0.425 AC: 6500 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3468

East Asian (EAS) AF: 0.457 AC: 2357 AN: 5158

South Asian (SAS) AF: 0.336 AC: 1618 AN: 4810

European-Finnish (FIN) AF: 0.367 AC: 3877 AN: 10570

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23928 AN: 67972

Other (OTH) AF: 0.405 AC: 855 AN: 2112

Alfa AF: 0.361 Hom.: 1245

Bravo AF: 0.389

Asia WGS AF: 0.467 AC: 1624 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.66
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs6123609; hg19: chr20-36971581;