13-109414835-T-C

Variant names:

• chr13-109414835-T-C
• rs9521355

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 0.804 in 152,096 control chromosomes in the GnomAD database, including 50,101 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 0.80 (50101 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.804 AC: 122257 AN: 151978 Hom.: 50064 Cov.: 32

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.804 AC: 122344 AN: 152096 Hom.: 50101 Cov.: 32 AF XY: 0.806 AC XY: 59950 AN XY: 74344

African (AFR) AF: 0.634 AC: 26276 AN: 41422

American (AMR) AF: 0.868 AC: 13275 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2705 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5187 AN: 5192

South Asian (SAS) AF: 0.825 AC: 3978 AN: 4820

European-Finnish (FIN) AF: 0.875 AC: 9249 AN: 10574

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58914 AN: 68006

Other (OTH) AF: 0.799 AC: 1685 AN: 2108

Alfa AF: 0.847 Hom.: 34056

Bravo AF: 0.800

Asia WGS AF: 0.917 AC: 3191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.092
DANN	Benign	0.31
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs9521355; hg19: chr13-110067182;