7-8959451-C-T

Variant names:

• chr7-8959451-C-T
• rs16874905

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 0.209 in 152,018 control chromosomes in the GnomAD database, including 3,798 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 0.21 (3798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31699 AN: 151900 Hom.: 3792 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.209 AC: 31713 AN: 152018 Hom.: 3798 Cov.: 32 AF XY: 0.212 AC XY: 15760 AN XY: 74296

African (AFR) AF: 0.113 AC: 4688 AN: 41492

American (AMR) AF: 0.317 AC: 4845 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 778 AN: 3470

East Asian (EAS) AF: 0.159 AC: 822 AN: 5162

South Asian (SAS) AF: 0.290 AC: 1397 AN: 4814

European-Finnish (FIN) AF: 0.249 AC: 2629 AN: 10556

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15806 AN: 67942

Other (OTH) AF: 0.213 AC: 450 AN: 2112

Alfa AF: 0.217 Hom.: 2651

Bravo AF: 0.208

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.45
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs16874905; hg19: chr7-8999081;