chr13-102929980-T-C

Variant names:

• chr13-102929980-T-C
• rs783447

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 0.335 in 151,990 control chromosomes in the GnomAD database, including 9,623 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 0.34 (9623 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.02
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50903 AN: 151872 Hom.: 9605 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.335 AC: 50937 AN: 151990 Hom.: 9623 Cov.: 32 AF XY: 0.331 AC XY: 24602 AN XY: 74298

African (AFR) AF: 0.514 AC: 21281 AN: 41426

American (AMR) AF: 0.228 AC: 3484 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1064 AN: 5158

South Asian (SAS) AF: 0.236 AC: 1140 AN: 4824

European-Finnish (FIN) AF: 0.284 AC: 2997 AN: 10568

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19168 AN: 67950

Other (OTH) AF: 0.289 AC: 608 AN: 2106

Alfa AF: 0.256 Hom.: 1263

Bravo AF: 0.336

Asia WGS AF: 0.216 AC: 753 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	0.074
DANN	Benign	0.41
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs783447; hg19: chr13-103582330;