chr13-28299770-T-C

Variant names:

• chr13-28299770-T-C
• rs1830792

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 0.136 in 152,238 control chromosomes in the GnomAD database, including 1,809 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 0.14 (1809 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 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: 0.136 AC: 20673 AN: 152120 Hom.: 1809 Cov.: 32

Gnomad AFR AF: 0.0323

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.136 AC: 20671 AN: 152238 Hom.: 1809 Cov.: 32 AF XY: 0.137 AC XY: 10231 AN XY: 74434

African (AFR) AF: 0.0322 AC: 1338 AN: 41578

American (AMR) AF: 0.192 AC: 2934 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 968 AN: 3464

East Asian (EAS) AF: 0.189 AC: 977 AN: 5174

South Asian (SAS) AF: 0.267 AC: 1287 AN: 4824

European-Finnish (FIN) AF: 0.108 AC: 1142 AN: 10600

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11481 AN: 67990

Other (OTH) AF: 0.159 AC: 336 AN: 2114

Alfa AF: 0.168 Hom.: 4530

Bravo AF: 0.135

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.76
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1830792; hg19: chr13-28873907;