rs1357365

Variant names:

• chr17-36109139-G-A
• rs1357365

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 0.308 in 152,016 control chromosomes in the GnomAD database, including 7,359 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 0.31 (7359 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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: 0.308 AC: 46846 AN: 151898 Hom.: 7344 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.308 AC: 46895 AN: 152016 Hom.: 7359 Cov.: 33 AF XY: 0.303 AC XY: 22485 AN XY: 74286

African (AFR) AF: 0.354 AC: 14666 AN: 41436

American (AMR) AF: 0.278 AC: 4242 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 863 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1636 AN: 5170

South Asian (SAS) AF: 0.312 AC: 1503 AN: 4822

European-Finnish (FIN) AF: 0.200 AC: 2106 AN: 10544

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20725 AN: 67982

Other (OTH) AF: 0.312 AC: 658 AN: 2110

Alfa AF: 0.309 Hom.: 23047

Bravo AF: 0.317

Asia WGS AF: 0.346 AC: 1203 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.25
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs1357365; hg19: chr17-34436532;