chr15-79573610-T-C

Variant names:

• chr15-79573610-T-C
• rs6495420

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 0.202 in 152,250 control chromosomes in the GnomAD database, including 3,251 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 0.20 (3251 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 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: 0.202 AC: 30793 AN: 152132 Hom.: 3243 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.202 AC: 30816 AN: 152250 Hom.: 3251 Cov.: 33 AF XY: 0.205 AC XY: 15267 AN XY: 74438

African (AFR) AF: 0.168 AC: 6987 AN: 41558

American (AMR) AF: 0.278 AC: 4244 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3470

East Asian (EAS) AF: 0.266 AC: 1380 AN: 5180

South Asian (SAS) AF: 0.285 AC: 1375 AN: 4826

European-Finnish (FIN) AF: 0.190 AC: 2017 AN: 10614

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13337 AN: 67994

Other (OTH) AF: 0.204 AC: 431 AN: 2112

Alfa AF: 0.196 Hom.: 3974

Bravo AF: 0.204

Asia WGS AF: 0.266 AC: 922 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	0.42
DANN	Benign	0.64
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs6495420; hg19: chr15-79865952;