chr3-15253857-A-G

Variant names:

• chr3-15253857-A-G
• rs1318937

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 0.249 in 152,130 control chromosomes in the GnomAD database, including 6,922 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 0.25 (6922 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 18 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 (AFR) allele frequency at 95% confidence interval = 0.49 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: 0.248 AC: 37773 AN: 152012 Hom.: 6888 Cov.: 32

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.0735

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.0902

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.249 AC: 37853 AN: 152130 Hom.: 6922 Cov.: 32 AF XY: 0.248 AC XY: 18459 AN XY: 74382

African (AFR) AF: 0.496 AC: 20552 AN: 41450

American (AMR) AF: 0.228 AC: 3479 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0735 AC: 255 AN: 3468

East Asian (EAS) AF: 0.423 AC: 2191 AN: 5174

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4824

European-Finnish (FIN) AF: 0.0902 AC: 957 AN: 10610

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8595 AN: 68002

Other (OTH) AF: 0.235 AC: 498 AN: 2116

Alfa AF: 0.177 Hom.: 9957

Bravo AF: 0.271

Asia WGS AF: 0.375 AC: 1302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.42
DANN	Benign	0.45
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1318937; hg19: chr3-15295364;