7-8872151-C-A

Variant names:

• chr7-8872151-C-A
• rs10486265

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;