rs1915279

Variant names:

• chr1-238912414-A-G
• rs1915279

Your query was ambiguous. Multiple possible variants found:

• chr1-238912414-A-G
• chr1-238912414-A-T

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 0.675 in 151,968 control chromosomes in the GnomAD database, including 36,618 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 0.68 (36618 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 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: 0.676 AC: 102616 AN: 151850 Hom.: 36624 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.675 AC: 102639 AN: 151968 Hom.: 36618 Cov.: 31 AF XY: 0.683 AC XY: 50744 AN XY: 74298

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.674

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.844

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.700

Alfa AF: 0.763 Hom.: 60591

Bravo AF: 0.652

Asia WGS AF: 0.819 AC: 2849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1915279; hg19: chr1-239075714;