rs1927384

Variant names:

• chr13-102493400-A-G
• rs1927384

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 0.166 in 152,132 control chromosomes in the GnomAD database, including 2,142 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 0.17 (2142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.219 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: 0.166 AC: 25293 AN: 152014 Hom.: 2144 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0804

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.166 AC: 25303 AN: 152132 Hom.: 2142 Cov.: 32 AF XY: 0.170 AC XY: 12672 AN XY: 74358

African (AFR) AF: 0.163 AC: 6776 AN: 41514

American (AMR) AF: 0.176 AC: 2683 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 392 AN: 3468

East Asian (EAS) AF: 0.202 AC: 1045 AN: 5178

South Asian (SAS) AF: 0.230 AC: 1109 AN: 4818

European-Finnish (FIN) AF: 0.229 AC: 2423 AN: 10566

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10397 AN: 68002

Other (OTH) AF: 0.176 AC: 371 AN: 2110

Alfa AF: 0.161 Hom.: 1154

Bravo AF: 0.166

Asia WGS AF: 0.197 AC: 683 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.69
DANN	Benign	0.45
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1927384; hg19: chr13-103145750;