rs10486715

Variant names:

• chr7-41439010-G-A
• rs10486715

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 0.139 in 152,168 control chromosomes in the GnomAD database, including 3,619 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 0.14 (3619 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.58

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.396 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: 0.138 AC: 21055 AN: 152050 Hom.: 3597 Cov.: 33

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0525

Gnomad ASJ AF: 0.0136

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0260

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0297

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.139 AC: 21106 AN: 152168 Hom.: 3619 Cov.: 33 AF XY: 0.134 AC XY: 9982 AN XY: 74406

Gnomad4 AFR AF: 0.401

Gnomad4 AMR AF: 0.0524

Gnomad4 ASJ AF: 0.0136

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.0112

Gnomad4 FIN AF: 0.0260

Gnomad4 NFE AF: 0.0297

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0506 Hom.: 811

Bravo AF: 0.154

Asia WGS AF: 0.0970 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	19
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486715; hg19: chr7-41478608; COSMIC: COSV63943843;