7-97600466-C-T

Variant names:

• chr7-97600466-C-T
• rs10486003

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 0.0878 in 152,206 control chromosomes in the GnomAD database, including 799 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 0.088 (799 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.10
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.223 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: 0.0879 AC: 13365 AN: 152088 Hom.: 799 Cov.: 33

Gnomad AFR AF: 0.0218

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0916

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0985

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

GnomAD4 genome AF: 0.0878 AC: 13369 AN: 152206 Hom.: 799 Cov.: 33 AF XY: 0.0879 AC XY: 6540 AN XY: 74416

African (AFR) AF: 0.0217 AC: 903 AN: 41528

American (AMR) AF: 0.122 AC: 1863 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 355 AN: 3470

East Asian (EAS) AF: 0.234 AC: 1208 AN: 5172

South Asian (SAS) AF: 0.149 AC: 716 AN: 4820

European-Finnish (FIN) AF: 0.0916 AC: 970 AN: 10586

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7117 AN: 68016

Other (OTH) AF: 0.0989 AC: 209 AN: 2114

Alfa AF: 0.100 Hom.: 2766

Bravo AF: 0.0878

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.41
DANN	Benign	0.46
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs10486003; hg19: chr7-97229778;