rs6037744

Variant names:

• chr20-4069044-G-A
• rs6037744

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 0.503 in 151,926 control chromosomes in the GnomAD database, including 19,488 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 0.50 (19488 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76325 AN: 151808 Hom.: 19488 Cov.: 31

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.503 AC: 76360 AN: 151926 Hom.: 19488 Cov.: 31 AF XY: 0.505 AC XY: 37524 AN XY: 74240

African (AFR) AF: 0.425 AC: 17612 AN: 41404

American (AMR) AF: 0.566 AC: 8646 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1905 AN: 3472

East Asian (EAS) AF: 0.620 AC: 3194 AN: 5154

South Asian (SAS) AF: 0.496 AC: 2391 AN: 4816

European-Finnish (FIN) AF: 0.524 AC: 5521 AN: 10540

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.518 AC: 35209 AN: 67956

Other (OTH) AF: 0.512 AC: 1078 AN: 2104

Alfa AF: 0.500 Hom.: 14472

Bravo AF: 0.507

Asia WGS AF: 0.544 AC: 1893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.69
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs6037744; hg19: chr20-4049691;