rs1872304

Variant names:

• chr15-48366591-A-G
• rs1872304

Your query was ambiguous. Multiple possible variants found:

• chr15-48366591-A-G
• chr15-48366591-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 0.703 in 152,062 control chromosomes in the GnomAD database, including 39,600 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 0.70 (39600 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

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 (NFE) allele frequency at 95% confidence interval = 0.823 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: 0.704 AC: 106933 AN: 151944 Hom.: 39603 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.828

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.703 AC: 106971 AN: 152062 Hom.: 39600 Cov.: 32 AF XY: 0.702 AC XY: 52190 AN XY: 74334

Gnomad4 AFR AF: 0.473

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.807

Gnomad4 NFE AF: 0.828

Gnomad4 OTH AF: 0.716

Alfa AF: 0.750 Hom.: 5398

Bravo AF: 0.692

Asia WGS AF: 0.550 AC: 1914 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	1.7
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1872304; hg19: chr15-48658788;