chr5-23395796-T-C

Variant names:

• chr5-23395796-T-C
• rs10038792

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 0.184 in 152,104 control chromosomes in the GnomAD database, including 2,827 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 0.18 (2827 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.184 AC: 28009 AN: 151986 Hom.: 2821 Cov.: 33

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.184 AC: 28041 AN: 152104 Hom.: 2827 Cov.: 33 AF XY: 0.185 AC XY: 13746 AN XY: 74342

African (AFR) AF: 0.244 AC: 10132 AN: 41526

American (AMR) AF: 0.154 AC: 2358 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 615 AN: 3468

East Asian (EAS) AF: 0.187 AC: 965 AN: 5166

South Asian (SAS) AF: 0.383 AC: 1846 AN: 4816

European-Finnish (FIN) AF: 0.140 AC: 1485 AN: 10576

Middle Eastern (MID) AF: 0.196 AC: 55 AN: 280

European-Non Finnish (NFE) AF: 0.148 AC: 10084 AN: 67970

Other (OTH) AF: 0.199 AC: 418 AN: 2104

Alfa AF: 0.167 Hom.: 1029

Bravo AF: 0.183

Asia WGS AF: 0.302 AC: 1034 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.5
DANN	Benign	0.60
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs10038792; hg19: chr5-23395905;