17-1761175-T-C

Variant names:

• chr17-1761175-T-C
• rs12150053

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 0.269 in 146,842 control chromosomes in the GnomAD database, including 6,540 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 0.27 (6540 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 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: 0.269 AC: 39472 AN: 146732 Hom.: 6545 Cov.: 28

Gnomad AFR AF: 0.0772

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.360

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.269 AC: 39459 AN: 146842 Hom.: 6540 Cov.: 28 AF XY: 0.267 AC XY: 19062 AN XY: 71440

African (AFR) AF: 0.0770 AC: 2980 AN: 38714

American (AMR) AF: 0.232 AC: 3411 AN: 14706

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1205 AN: 3460

East Asian (EAS) AF: 0.280 AC: 1394 AN: 4980

South Asian (SAS) AF: 0.243 AC: 1140 AN: 4692

European-Finnish (FIN) AF: 0.317 AC: 3083 AN: 9720

Middle Eastern (MID) AF: 0.356 AC: 101 AN: 284

European-Non Finnish (NFE) AF: 0.372 AC: 25078 AN: 67352

Other (OTH) AF: 0.288 AC: 585 AN: 2034

Alfa AF: 0.164 Hom.: 442

Bravo AF: 0.250

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.5
DANN	Benign	0.32
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs12150053; hg19: chr17-1664469;