rs6024836

Variant names:

• chr20-56369012-G-A
• rs6024836

Your query was ambiguous. Multiple possible variants found:

• chr20-56369012-G-A
• chr20-56369012-G-C
• chr20-56369012-G-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 0.417 in 151,936 control chromosomes in the GnomAD database, including 15,694 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 0.42 (15694 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

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 (AFR) allele frequency at 95% confidence interval = 0.667 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: 0.417 AC: 63306 AN: 151818 Hom.: 15644 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.417 AC: 63408 AN: 151936 Hom.: 15694 Cov.: 32 AF XY: 0.422 AC XY: 31317 AN XY: 74252

Gnomad4 AFR AF: 0.674

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.388

Alfa AF: 0.296 Hom.: 11940

Bravo AF: 0.433

Asia WGS AF: 0.504 AC: 1751 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	0.024
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6024836; hg19: chr20-54944068;