chr7-8932422-C-G

Variant names:

• chr7-8932422-C-G
• rs10486270

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 0.271 in 151,774 control chromosomes in the GnomAD database, including 6,124 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 0.27 (6124 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.326 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: 0.271 AC: 41113 AN: 151656 Hom.: 6122 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.0855

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.271 AC: 41141 AN: 151774 Hom.: 6124 Cov.: 32 AF XY: 0.266 AC XY: 19772 AN XY: 74208

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.0859

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.296

Alfa AF: 0.183 Hom.: 422

Bravo AF: 0.271

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486270; hg19: chr7-8972052;