rs930268

Variant names:

• chr13-104600319-G-A
• rs930268

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 0.234 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
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.306 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: 0.234 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

African (AFR) AF: 0.103 AC: 4258 AN: 41480

American (AMR) AF: 0.281 AC: 4280 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3464

East Asian (EAS) AF: 0.271 AC: 1400 AN: 5160

South Asian (SAS) AF: 0.0974 AC: 470 AN: 4826

European-Finnish (FIN) AF: 0.255 AC: 2693 AN: 10560

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21031 AN: 67956

Other (OTH) AF: 0.247 AC: 522 AN: 2112

Alfa AF: 0.270 Hom.: 1047

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
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs930268; hg19: chr13-105252670;