rs1834640

Variant names:

• chr15-48099968-A-G
• rs1834640

Your query was ambiguous. Multiple possible variants found:

• chr15-48099968-A-G
• chr15-48099968-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 0.291 in 152,150 control chromosomes in the GnomAD database, including 16,501 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 0.29 (16501 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.402

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.881 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: 0.290 AC: 44095 AN: 152032 Hom.: 16436 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.0142

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00803

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.291 AC: 44226 AN: 152150 Hom.: 16501 Cov.: 32 AF XY: 0.291 AC XY: 21684 AN XY: 74416

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.0107

Gnomad4 EAS AF: 0.903

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.0142

Gnomad4 NFE AF: 0.00803

Gnomad4 OTH AF: 0.228

Alfa AF: 0.0759 Hom.: 8029

Bravo AF: 0.336

Asia WGS AF: 0.658 AC: 2285 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	9.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1834640; hg19: chr15-48392165;