rs10487867

Variant names:

• chr7-83888815-G-A
• rs10487867

Your query was ambiguous. Multiple possible variants found:

• chr7-83888815-G-A
• chr7-83888815-G-C
• chr7-83888815-G-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 0.366 in 151,682 control chromosomes in the GnomAD database, including 11,241 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 0.37 (11241 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

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 = 0.432 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: 0.366 AC: 55525 AN: 151562 Hom.: 11228 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.366 AC: 55564 AN: 151682 Hom.: 11241 Cov.: 32 AF XY: 0.372 AC XY: 27588 AN XY: 74116

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.359

Alfa AF: 0.421 Hom.: 19730

Bravo AF: 0.352

Asia WGS AF: 0.225 AC: 784 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.12
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487867; hg19: chr7-83518131;