chr7-97848799-C-G

Variant names:

• chr7-97848799-C-G
• rs10486009

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.256 AC: 10598 AN: 41324

American (AMR) AF: 0.126 AC: 1917 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 559 AN: 3466

East Asian (EAS) AF: 0.109 AC: 564 AN: 5172

South Asian (SAS) AF: 0.215 AC: 1031 AN: 4804

European-Finnish (FIN) AF: 0.100 AC: 1056 AN: 10508

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9505 AN: 67964

Other (OTH) AF: 0.180 AC: 379 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.032
DANN	Benign	0.67
PhyloP100		-3.9

Splicing

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

Other links and lift over

dbSNP: rs10486009; hg19: chr7-97478111;