3-172450502-A-G

Variant names:

• chr3-172450502-A-G
• rs2981464

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 0.553 in 151,992 control chromosomes in the GnomAD database, including 23,620 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 0.55 (23620 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 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: 0.553 AC: 83923 AN: 151874 Hom.: 23596 Cov.: 32

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.553 AC: 83992 AN: 151992 Hom.: 23620 Cov.: 32 AF XY: 0.551 AC XY: 40927 AN XY: 74272

African (AFR) AF: 0.659 AC: 27310 AN: 41446

American (AMR) AF: 0.521 AC: 7954 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1945 AN: 3470

East Asian (EAS) AF: 0.389 AC: 2002 AN: 5148

South Asian (SAS) AF: 0.592 AC: 2848 AN: 4814

European-Finnish (FIN) AF: 0.522 AC: 5503 AN: 10546

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.509 AC: 34622 AN: 67982

Other (OTH) AF: 0.562 AC: 1186 AN: 2112

Alfa AF: 0.539 Hom.: 2768

Bravo AF: 0.556

Asia WGS AF: 0.544 AC: 1888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.65
DANN	Benign	0.19
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2981464; hg19: chr3-172168292;