rs9603616

Variant names:

• chr13-39793932-C-T
• rs9603616

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 0.297 in 151,980 control chromosomes in the GnomAD database, including 6,905 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 0.30 (6905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 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: 0.297 AC: 45095 AN: 151862 Hom.: 6911 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.297 AC: 45105 AN: 151980 Hom.: 6905 Cov.: 32 AF XY: 0.292 AC XY: 21688 AN XY: 74262

African (AFR) AF: 0.245 AC: 10161 AN: 41476

American (AMR) AF: 0.216 AC: 3298 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 720 AN: 3468

East Asian (EAS) AF: 0.226 AC: 1165 AN: 5154

South Asian (SAS) AF: 0.284 AC: 1366 AN: 4812

European-Finnish (FIN) AF: 0.340 AC: 3581 AN: 10540

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23865 AN: 67936

Other (OTH) AF: 0.296 AC: 625 AN: 2114

Alfa AF: 0.295 Hom.: 3948

Bravo AF: 0.283

Asia WGS AF: 0.256 AC: 891 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.92
DANN	Benign	0.44
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs9603616; hg19: chr13-40368069;