chr3-172021197-G-A

Variant names:

• chr3-172021197-G-A
• rs472728

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 0.503 in 151,952 control chromosomes in the GnomAD database, including 19,489 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 0.50 (19489 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.548 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: 0.503 AC: 76394 AN: 151834 Hom.: 19466 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.470

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.503 AC: 76462 AN: 151952 Hom.: 19489 Cov.: 32 AF XY: 0.508 AC XY: 37693 AN XY: 74268

African (AFR) AF: 0.432 AC: 17912 AN: 41424

American (AMR) AF: 0.552 AC: 8429 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.470 AC: 1631 AN: 3472

East Asian (EAS) AF: 0.542 AC: 2798 AN: 5166

South Asian (SAS) AF: 0.566 AC: 2725 AN: 4814

European-Finnish (FIN) AF: 0.608 AC: 6405 AN: 10532

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 35009 AN: 67960

Other (OTH) AF: 0.470 AC: 991 AN: 2108

Alfa AF: 0.505 Hom.: 42367

Bravo AF: 0.494

Asia WGS AF: 0.519 AC: 1804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.64
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs472728; hg19: chr3-171738987;