rs3761249

Variant names:

• chr20-3085716-T-G
• rs3761249

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 0.225 in 151,968 control chromosomes in the GnomAD database, including 6,288 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 0.23 (6288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 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: 0.225 AC: 34157 AN: 151850 Hom.: 6270 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.0620

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.225 AC: 34217 AN: 151968 Hom.: 6288 Cov.: 32 AF XY: 0.220 AC XY: 16350 AN XY: 74294

African (AFR) AF: 0.500 AC: 20707 AN: 41386

American (AMR) AF: 0.140 AC: 2132 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3472

East Asian (EAS) AF: 0.280 AC: 1441 AN: 5152

South Asian (SAS) AF: 0.193 AC: 930 AN: 4818

European-Finnish (FIN) AF: 0.0620 AC: 657 AN: 10600

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7057 AN: 67944

Other (OTH) AF: 0.215 AC: 454 AN: 2112

Alfa AF: 0.145 Hom.: 3062

Bravo AF: 0.242

Asia WGS AF: 0.240 AC: 834 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.74
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs3761249; hg19: chr20-3066362;