19-7658575-C-T

Variant names:

• chr19-7658575-C-T
• rs2081075

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 0.297 in 152,096 control chromosomes in the GnomAD database, including 7,042 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 0.30 (7042 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 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: 0.297 AC: 45139 AN: 151978 Hom.: 7035 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.297 AC: 45169 AN: 152096 Hom.: 7042 Cov.: 32 AF XY: 0.301 AC XY: 22402 AN XY: 74326

African (AFR) AF: 0.247 AC: 10252 AN: 41488

American (AMR) AF: 0.361 AC: 5512 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 913 AN: 3470

East Asian (EAS) AF: 0.514 AC: 2661 AN: 5176

South Asian (SAS) AF: 0.214 AC: 1034 AN: 4822

European-Finnish (FIN) AF: 0.360 AC: 3805 AN: 10578

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

European-Non Finnish (NFE) AF: 0.296 AC: 20116 AN: 67976

Other (OTH) AF: 0.301 AC: 636 AN: 2114

Alfa AF: 0.298 Hom.: 18219

Bravo AF: 0.302

Asia WGS AF: 0.331 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.9
DANN	Benign	0.76
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs2081075; hg19: chr19-7723461;