rs675302

Positions:

• chr13-85788633-C-G
• chr13-85788633-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.267 in 151,684 control chromosomes in the GnomAD database, including 6,247 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 (6247 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

ACMG classification

Verdict is Benign. Variant got -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 = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40463 AN: 151566 Hom.: 6235 Cov.: 33

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.630

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.267 AC: 40501 AN: 151684 Hom.: 6247 Cov.: 33 AF XY: 0.268 AC XY: 19879 AN XY: 74132

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.631

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.301

Alfa AF: 0.144 Hom.: 279

Bravo AF: 0.272

Asia WGS AF: 0.464 AC: 1611 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.66
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs675302; hg19: chr13-86362768;