chr13-90824277-T-C

Variant names:

• chr13-90824277-T-C
• rs9301694

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 0.27 in 152,014 control chromosomes in the GnomAD database, including 5,906 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 0.27 (5906 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.840
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.304 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41010 AN: 151894 Hom.: 5900 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.0906

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.270 AC: 41037 AN: 152014 Hom.: 5906 Cov.: 32 AF XY: 0.272 AC XY: 20200 AN XY: 74286

African (AFR) AF: 0.214 AC: 8895 AN: 41498

American (AMR) AF: 0.230 AC: 3510 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 866 AN: 3468

East Asian (EAS) AF: 0.0906 AC: 469 AN: 5176

South Asian (SAS) AF: 0.253 AC: 1222 AN: 4826

European-Finnish (FIN) AF: 0.382 AC: 4025 AN: 10540

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.308 AC: 20905 AN: 67928

Other (OTH) AF: 0.266 AC: 563 AN: 2114

Alfa AF: 0.279 Hom.: 2080

Bravo AF: 0.255

Asia WGS AF: 0.200 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.7
DANN	Benign	0.71
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs9301694; hg19: chr13-91476531;