chr17-7459040-T-C

Variant names:

• chr17-7459040-T-C
• rs17732878

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 0.183 in 152,236 control chromosomes in the GnomAD database, including 2,719 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 (2719 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.268 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: 0.183 AC: 27787 AN: 152118 Hom.: 2724 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0350

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.183 AC: 27787 AN: 152236 Hom.: 2719 Cov.: 33 AF XY: 0.181 AC XY: 13454 AN XY: 74428

African (AFR) AF: 0.160 AC: 6669 AN: 41554

American (AMR) AF: 0.147 AC: 2254 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 789 AN: 3468

East Asian (EAS) AF: 0.0351 AC: 182 AN: 5188

South Asian (SAS) AF: 0.280 AC: 1351 AN: 4826

European-Finnish (FIN) AF: 0.169 AC: 1793 AN: 10588

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13988 AN: 68000

Other (OTH) AF: 0.200 AC: 422 AN: 2112

Alfa AF: 0.182 Hom.: 1421

Bravo AF: 0.179

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.32
DANN	Benign	0.38
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs17732878; hg19: chr17-7362359;