3-21265909-T-G

Variant names:

• chr3-21265909-T-G
• rs1344870

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 0.0811 in 152,238 control chromosomes in the GnomAD database, including 1,387 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 0.081 (1387 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0810 AC: 12316 AN: 152120 Hom.: 1375 Cov.: 32

Gnomad AFR AF: 0.0605

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0261

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0323

Gnomad OTH AF: 0.0935

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

GnomAD4 genome AF: 0.0811 AC: 12352 AN: 152238 Hom.: 1387 Cov.: 32 AF XY: 0.0871 AC XY: 6488 AN XY: 74452

African (AFR) AF: 0.0606 AC: 2518 AN: 41544

American (AMR) AF: 0.319 AC: 4873 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3468

East Asian (EAS) AF: 0.251 AC: 1296 AN: 5170

South Asian (SAS) AF: 0.161 AC: 775 AN: 4826

European-Finnish (FIN) AF: 0.0261 AC: 277 AN: 10620

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0323 AC: 2197 AN: 68012

Other (OTH) AF: 0.0963 AC: 203 AN: 2108

Alfa AF: 0.0736 Hom.: 754

Bravo AF: 0.103

Asia WGS AF: 0.234 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.44
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs1344870; hg19: chr3-21307401;