rs6040449

Positions:

• chr20-11228874-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 0.658 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.725

Gnomad4 AMR AF: 0.664

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.665

Alfa AF: 0.643 Hom.: 40733

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6040449; hg19: chr20-11209522;