rs1476587

Variant names:

• chr7-87067398-A-G
• rs1476587

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.128 in 152,136 control chromosomes in the GnomAD database, including 1,375 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 0.13 (1375 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 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: 0.128 AC: 19412 AN: 152018 Hom.: 1372 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.128 AC: 19448 AN: 152136 Hom.: 1375 Cov.: 32 AF XY: 0.130 AC XY: 9677 AN XY: 74386

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.305

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.112

Alfa AF: 0.118 Hom.: 1015

Bravo AF: 0.128

Asia WGS AF: 0.253 AC: 874 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	8.8
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1476587; hg19: chr7-86696714;