rs17349283

Variant names:

• chr2-221225077-A-G
• rs17349283

Your query was ambiguous. Multiple possible variants found:

• chr2-221225077-A-G
• chr2-221225077-A-T

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 0.346 in 152,018 control chromosomes in the GnomAD database, including 11,095 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 0.35 (11095 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.670
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 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: 0.346 AC: 52597 AN: 151900 Hom.: 11096 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.346 AC: 52583 AN: 152018 Hom.: 11095 Cov.: 32 AF XY: 0.348 AC XY: 25848 AN XY: 74326

African (AFR) AF: 0.110 AC: 4560 AN: 41462

American (AMR) AF: 0.350 AC: 5354 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1312 AN: 3470

East Asian (EAS) AF: 0.216 AC: 1114 AN: 5158

South Asian (SAS) AF: 0.366 AC: 1757 AN: 4802

European-Finnish (FIN) AF: 0.547 AC: 5780 AN: 10566

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31616 AN: 67958

Other (OTH) AF: 0.345 AC: 729 AN: 2112

Alfa AF: 0.408 Hom.: 2389

Bravo AF: 0.320

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.69
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs17349283; hg19: chr2-222089797;