chr17-71382132-C-T

Variant names:

• chr17-71382132-C-T
• rs2190706

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 0.308 in 151,784 control chromosomes in the GnomAD database, including 7,931 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 0.31 (7931 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.534 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: 0.309 AC: 46815 AN: 151666 Hom.: 7927 Cov.: 31

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.308 AC: 46821 AN: 151784 Hom.: 7931 Cov.: 31 AF XY: 0.312 AC XY: 23129 AN XY: 74148

African (AFR) AF: 0.156 AC: 6460 AN: 41390

American (AMR) AF: 0.332 AC: 5064 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1321 AN: 3466

East Asian (EAS) AF: 0.551 AC: 2840 AN: 5152

South Asian (SAS) AF: 0.376 AC: 1811 AN: 4814

European-Finnish (FIN) AF: 0.381 AC: 4010 AN: 10530

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24148 AN: 67884

Other (OTH) AF: 0.333 AC: 702 AN: 2110

Alfa AF: 0.198 Hom.: 469

Bravo AF: 0.299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.84
DANN	Benign	0.50
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2190706; hg19: chr17-69378273;