rs17348202

Variant names:

• chr2-221207458-T-C
• rs17348202

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 0.0465 in 151,772 control chromosomes in the GnomAD database, including 207 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 0.046 (207 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.788

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.111 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: 0.0465 AC: 7055 AN: 151664 Hom.: 206 Cov.: 31

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.0574

Gnomad AMR AF: 0.0429

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0296

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.0596

Gnomad OTH AF: 0.0590

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

GnomAD4 genome AF: 0.0465 AC: 7057 AN: 151772 Hom.: 207 Cov.: 31 AF XY: 0.0464 AC XY: 3440 AN XY: 74118

Gnomad4 AFR AF: 0.0210

Gnomad4 AMR AF: 0.0431

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0296

Gnomad4 NFE AF: 0.0596

Gnomad4 OTH AF: 0.0585

Alfa AF: 0.0636 Hom.: 223

Bravo AF: 0.0452

Asia WGS AF: 0.0450 AC: 158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17348202; hg19: chr2-222072178;