rs1847202

Variant names:

• chr3-72885220-T-C
• rs1847202

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.404 in 152,076 control chromosomes in the GnomAD database, including 13,792 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 0.40 (13792 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 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: 0.404 AC: 61333 AN: 151958 Hom.: 13756 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.404 AC: 61436 AN: 152076 Hom.: 13792 Cov.: 32 AF XY: 0.397 AC XY: 29534 AN XY: 74342

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.374

Alfa AF: 0.390 Hom.: 1537

Bravo AF: 0.407

Asia WGS AF: 0.143 AC: 496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1847202; hg19: chr3-72934371;