7-83854663-C-T

Variant names:

• chr7-83854663-C-T
• rs4732523

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 0.32 in 151,846 control chromosomes in the GnomAD database, including 12,506 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 0.32 (12506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.125
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 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: 0.320 AC: 48547 AN: 151728 Hom.: 12467 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.320 AC: 48630 AN: 151846 Hom.: 12506 Cov.: 32 AF XY: 0.316 AC XY: 23448 AN XY: 74200

African (AFR) AF: 0.680 AC: 28140 AN: 41396

American (AMR) AF: 0.303 AC: 4608 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 491 AN: 3466

East Asian (EAS) AF: 0.692 AC: 3567 AN: 5152

South Asian (SAS) AF: 0.134 AC: 645 AN: 4824

European-Finnish (FIN) AF: 0.106 AC: 1113 AN: 10544

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9200 AN: 67932

Other (OTH) AF: 0.319 AC: 674 AN: 2110

Alfa AF: 0.137 Hom.: 1064

Bravo AF: 0.357

Asia WGS AF: 0.436 AC: 1516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.89
DANN	Benign	0.48
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs4732523; hg19: chr7-83483979;