rs10486009

chr7-97848799-C-Gchr7-97848799-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 0.17 in 151,806 control chromosomes in the GnomAD database, including 2,412 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 0.17 (2412 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.86

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 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: 0.170 AC: 25772 AN: 151688 Hom.: 2406 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.170 AC: 25812 AN: 151806 Hom.: 2412 Cov.: 32 AF XY: 0.168 AC XY: 12440 AN XY: 74180

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.215

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.180

Alfa AF: 0.0657 Hom.: 71

Bravo AF: 0.172

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.032
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10486009; hg19: chr7-97478111;