3-20037997-G-C

Variant names:

• chr3-20037997-G-C
• rs2948080

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 0.283 in 152,146 control chromosomes in the GnomAD database, including 6,587 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 0.28 (6587 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43075 AN: 152028 Hom.: 6589 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.283 AC: 43094 AN: 152146 Hom.: 6587 Cov.: 33 AF XY: 0.286 AC XY: 21247 AN XY: 74350

African (AFR) AF: 0.184 AC: 7623 AN: 41532

American (AMR) AF: 0.334 AC: 5111 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 765 AN: 3468

East Asian (EAS) AF: 0.496 AC: 2574 AN: 5186

South Asian (SAS) AF: 0.332 AC: 1600 AN: 4822

European-Finnish (FIN) AF: 0.303 AC: 3202 AN: 10556

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21423 AN: 67978

Other (OTH) AF: 0.288 AC: 609 AN: 2114

Alfa AF: 0.292 Hom.: 822

Bravo AF: 0.281

Asia WGS AF: 0.405 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.5
DANN	Benign	0.67
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2948080; hg19: chr3-20079489;