chr13-27503007-G-C

Variant names:

• chr13-27503007-G-C
• rs9512730

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 0.246 in 152,040 control chromosomes in the GnomAD database, including 4,698 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 0.25 (4698 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.190
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 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: 0.246 AC: 37436 AN: 151922 Hom.: 4700 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.246 AC: 37442 AN: 152040 Hom.: 4698 Cov.: 31 AF XY: 0.243 AC XY: 18047 AN XY: 74306

African (AFR) AF: 0.231 AC: 9578 AN: 41450

American (AMR) AF: 0.252 AC: 3858 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3462

East Asian (EAS) AF: 0.125 AC: 645 AN: 5170

South Asian (SAS) AF: 0.130 AC: 628 AN: 4814

European-Finnish (FIN) AF: 0.277 AC: 2926 AN: 10576

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18125 AN: 67966

Other (OTH) AF: 0.223 AC: 470 AN: 2108

Alfa AF: 0.260 Hom.: 681

Bravo AF: 0.246

Asia WGS AF: 0.123 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.73
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs9512730; hg19: chr13-28077144;