rs322957

Variant names:

• chr17-3558836-T-A
• rs322957

Your query was ambiguous. Multiple possible variants found:

• chr17-3558836-T-A
• chr17-3558836-T-C

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 0.291 in 152,126 control chromosomes in the GnomAD database, including 7,461 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 0.29 (7461 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.810
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 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: 0.291 AC: 44271 AN: 152008 Hom.: 7454 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.291 AC: 44313 AN: 152126 Hom.: 7461 Cov.: 33 AF XY: 0.293 AC XY: 21792 AN XY: 74360

African (AFR) AF: 0.115 AC: 4779 AN: 41532

American (AMR) AF: 0.335 AC: 5128 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1164 AN: 3468

East Asian (EAS) AF: 0.277 AC: 1434 AN: 5172

South Asian (SAS) AF: 0.424 AC: 2044 AN: 4818

European-Finnish (FIN) AF: 0.312 AC: 3297 AN: 10566

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25314 AN: 67968

Other (OTH) AF: 0.316 AC: 667 AN: 2110

Alfa AF: 0.192 Hom.: 456

Bravo AF: 0.283

Asia WGS AF: 0.342 AC: 1189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.75
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs322957; hg19: chr17-3462130;