rs1575633

Positions:

• chr13-105395212-C-A

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 0.322 in 151,880 control chromosomes in the GnomAD database, including 8,019 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 0.32 (8019 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.442

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 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: 0.322 AC: 48859 AN: 151762 Hom.: 8006 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.322 AC: 48909 AN: 151880 Hom.: 8019 Cov.: 32 AF XY: 0.324 AC XY: 24086 AN XY: 74240

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.312

Alfa AF: 0.300 Hom.: 1571

Bravo AF: 0.324

Asia WGS AF: 0.282 AC: 983 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	2.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1575633; hg19: chr13-106047562;