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. The variant received -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
• Publications: 24 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 (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

African (AFR) AF: 0.674 AC: 27895 AN: 41410

American (AMR) AF: 0.423 AC: 6458 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 973 AN: 3460

East Asian (EAS) AF: 0.632 AC: 3255 AN: 5150

South Asian (SAS) AF: 0.381 AC: 1836 AN: 4816

European-Finnish (FIN) AF: 0.390 AC: 4116 AN: 10544

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17717 AN: 67966

Other (OTH) AF: 0.388 AC: 820 AN: 2116

Alfa AF: 0.320 Hom.: 35555

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6024836; hg19: chr20-54944068;