13-97856624-C-T

Variant names:

• chr13-97856624-C-T
• rs16954586

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 0.076 in 152,168 control chromosomes in the GnomAD database, including 619 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 0.076 (619 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 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: 0.0761 AC: 11578 AN: 152050 Hom.: 619 Cov.: 32

Gnomad AFR AF: 0.0187

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0791

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.0602

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0940

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.0760 AC: 11568 AN: 152168 Hom.: 619 Cov.: 32 AF XY: 0.0778 AC XY: 5785 AN XY: 74392

African (AFR) AF: 0.0186 AC: 774 AN: 41532

American (AMR) AF: 0.0789 AC: 1207 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 453 AN: 3470

East Asian (EAS) AF: 0.139 AC: 716 AN: 5154

South Asian (SAS) AF: 0.236 AC: 1135 AN: 4810

European-Finnish (FIN) AF: 0.0602 AC: 638 AN: 10590

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0939 AC: 6388 AN: 67994

Other (OTH) AF: 0.0928 AC: 196 AN: 2112

Alfa AF: 0.0922 Hom.: 882

Bravo AF: 0.0707

Asia WGS AF: 0.155 AC: 539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.31
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs16954586; hg19: chr13-98508878;