13-55399151-T-C

Variant names:

• chr13-55399151-T-C
• rs9316790

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 0.105 in 151,552 control chromosomes in the GnomAD database, including 1,176 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 0.11 (1176 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382
• Publications: 1 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 = 0.202 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: 0.105 AC: 15945 AN: 151434 Hom.: 1171 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0821

Gnomad ASJ AF: 0.0396

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.0909

Gnomad FIN AF: 0.0625

Gnomad MID AF: 0.0613

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.0821

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

GnomAD4 genome AF: 0.105 AC: 15971 AN: 151552 Hom.: 1176 Cov.: 32 AF XY: 0.105 AC XY: 7759 AN XY: 74094

African (AFR) AF: 0.206 AC: 8526 AN: 41448

American (AMR) AF: 0.0820 AC: 1244 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.0396 AC: 137 AN: 3458

East Asian (EAS) AF: 0.0465 AC: 241 AN: 5182

South Asian (SAS) AF: 0.0915 AC: 442 AN: 4828

European-Finnish (FIN) AF: 0.0625 AC: 663 AN: 10600

Middle Eastern (MID) AF: 0.0625 AC: 18 AN: 288

European-Non Finnish (NFE) AF: 0.0665 AC: 4492 AN: 67568

Other (OTH) AF: 0.0851 AC: 179 AN: 2104

Alfa AF: 0.0953 Hom.: 122

Bravo AF: 0.112

Asia WGS AF: 0.0860 AC: 299 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.72
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs9316790; hg19: chr13-55973286;