rs1915250

Variant names:

• chr1-239020474-C-T
• rs1915250

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 0.0785 in 152,040 control chromosomes in the GnomAD database, including 665 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 0.078 (665 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.11 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: 0.0785 AC: 11931 AN: 151922 Hom.: 666 Cov.: 31

Gnomad AFR AF: 0.0211

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.00194

Gnomad SAS AF: 0.0274

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0780

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

GnomAD4 genome AF: 0.0785 AC: 11928 AN: 152040 Hom.: 665 Cov.: 31 AF XY: 0.0776 AC XY: 5766 AN XY: 74316

African (AFR) AF: 0.0211 AC: 874 AN: 41514

American (AMR) AF: 0.115 AC: 1750 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.0757 AC: 262 AN: 3462

East Asian (EAS) AF: 0.00194 AC: 10 AN: 5150

South Asian (SAS) AF: 0.0282 AC: 136 AN: 4822

European-Finnish (FIN) AF: 0.137 AC: 1451 AN: 10602

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7177 AN: 67936

Other (OTH) AF: 0.0777 AC: 164 AN: 2112

Alfa AF: 0.0912 Hom.: 670

Bravo AF: 0.0775

Asia WGS AF: 0.0190 AC: 66 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.70
DANN	Benign	0.22
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1915250; hg19: chr1-239183774;