rs6040449

Variant names:

• chr20-11228874-G-A
• rs6040449

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 0.658 in 152,076 control chromosomes in the GnomAD database, including 33,181 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 0.66 (33181 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.718 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: 0.658 AC: 99940 AN: 151958 Hom.: 33135 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.658 AC: 100047 AN: 152076 Hom.: 33181 Cov.: 32 AF XY: 0.658 AC XY: 48911 AN XY: 74326

African (AFR) AF: 0.725 AC: 30067 AN: 41480

American (AMR) AF: 0.664 AC: 10149 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2405 AN: 3472

East Asian (EAS) AF: 0.520 AC: 2690 AN: 5174

South Asian (SAS) AF: 0.643 AC: 3103 AN: 4826

European-Finnish (FIN) AF: 0.601 AC: 6338 AN: 10554

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43076 AN: 67972

Other (OTH) AF: 0.665 AC: 1405 AN: 2114

Alfa AF: 0.645 Hom.: 57583

Bravo AF: 0.661

Asia WGS AF: 0.617 AC: 2145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.85
DANN	Benign	0.40
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs6040449; hg19: chr20-11209522;