rs10486265

chr7-8872151-C-Achr7-8872151-C-Gchr7-8872151-C-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 0.056 in 151,930 control chromosomes in the GnomAD database, including 573 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 0.056 (573 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.663

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 (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0558 AC: 8464 AN: 151812 Hom.: 565 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0646

Gnomad ASJ AF: 0.00751

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.0731

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00895

Gnomad OTH AF: 0.0459

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

GnomAD4 genome AF: 0.0560 AC: 8508 AN: 151930 Hom.: 573 Cov.: 32 AF XY: 0.0602 AC XY: 4468 AN XY: 74276

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0652

Gnomad4 ASJ AF: 0.00751

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.0460

Gnomad4 FIN AF: 0.0731

Gnomad4 NFE AF: 0.00895

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0150 Hom.: 9

Bravo AF: 0.0621

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.043
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486265; hg19: chr7-8911781;