rs930268

Positions:

• chr13-104600319-G-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 0.234 in 151,994 control chromosomes in the GnomAD database, including 4,739 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 0.23 (4739 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.514

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 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: 0.234 AC: 35571 AN: 151876 Hom.: 4739 Cov.: 32

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.0961

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.234 AC: 35573 AN: 151994 Hom.: 4739 Cov.: 32 AF XY: 0.230 AC XY: 17079 AN XY: 74264

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.0974

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.247

Alfa AF: 0.275 Hom.: 1044

Bravo AF: 0.236

Asia WGS AF: 0.160 AC: 558 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.55
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs930268; hg19: chr13-105252670;