rs6124601

Variant names:

• chr20-43859616-A-C
• rs6124601

Your query was ambiguous. Multiple possible variants found:

• chr20-43859616-A-C
• chr20-43859616-A-G
• chr20-43859616-A-T

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 0.285 in 152,098 control chromosomes in the GnomAD database, including 6,927 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 0.29 (6927 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.511 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: 0.285 AC: 43351 AN: 151980 Hom.: 6902 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.285 AC: 43423 AN: 152098 Hom.: 6927 Cov.: 32 AF XY: 0.293 AC XY: 21779 AN XY: 74354

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.215

Gnomad4 OTH AF: 0.286

Alfa AF: 0.242 Hom.: 6154

Bravo AF: 0.298

Asia WGS AF: 0.445 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6124601; hg19: chr20-42488256;