13-109406284-T-C

Variant names:

• chr13-109406284-T-C
• rs1328250

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 0.803 in 152,138 control chromosomes in the GnomAD database, including 50,001 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 (50001 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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: 122149 AN: 152020 Hom.: 49965 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.866

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.803 AC: 122235 AN: 152138 Hom.: 50001 Cov.: 31 AF XY: 0.805 AC XY: 59888 AN XY: 74362

African (AFR) AF: 0.631 AC: 26182 AN: 41468

American (AMR) AF: 0.866 AC: 13247 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2701 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5165 AN: 5170

South Asian (SAS) AF: 0.828 AC: 3986 AN: 4812

European-Finnish (FIN) AF: 0.875 AC: 9262 AN: 10590

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.866 AC: 58930 AN: 68014

Other (OTH) AF: 0.798 AC: 1686 AN: 2112

Alfa AF: 0.834 Hom.: 9052

Bravo AF: 0.799

Asia WGS AF: 0.916 AC: 3187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.29
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs1328250; hg19: chr13-110058631;