rs7359623

Variant names:

• chr17-39893336-C-T
• rs7359623

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 0.441 in 152,022 control chromosomes in the GnomAD database, including 15,199 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 0.44 (15199 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388
• Publications: 29 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66991 AN: 151904 Hom.: 15180 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.441 AC: 67059 AN: 152022 Hom.: 15199 Cov.: 32 AF XY: 0.443 AC XY: 32891 AN XY: 74290

African (AFR) AF: 0.360 AC: 14904 AN: 41454

American (AMR) AF: 0.418 AC: 6381 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1505 AN: 3464

East Asian (EAS) AF: 0.271 AC: 1401 AN: 5174

South Asian (SAS) AF: 0.388 AC: 1868 AN: 4814

European-Finnish (FIN) AF: 0.573 AC: 6051 AN: 10568

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33337 AN: 67966

Other (OTH) AF: 0.425 AC: 895 AN: 2106

Alfa AF: 0.426 Hom.: 3312

Bravo AF: 0.419

Asia WGS AF: 0.394 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.8
DANN	Benign	0.37
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs7359623; hg19: chr17-38049589;