rs6123609

Variant names:

• chr20-38343178-G-C
• rs6123609

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 0.376 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.405

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6123609; hg19: chr20-36971581;