rs6037744

Positions:

• chr20-4069044-G-A

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 0.503 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.496

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.512

Alfa AF: 0.512 Hom.: 9066

Bravo AF: 0.507

Asia WGS AF: 0.544 AC: 1893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6037744; hg19: chr20-4049691;