chr17-29220208-G-C

Variant names:

• chr17-29220208-G-C
• rs1018190

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 0.383 in 152,122 control chromosomes in the GnomAD database, including 11,486 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 0.38 (11486 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 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: 0.383 AC: 58206 AN: 152004 Hom.: 11480 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.383 AC: 58226 AN: 152122 Hom.: 11486 Cov.: 33 AF XY: 0.378 AC XY: 28120 AN XY: 74362

African (AFR) AF: 0.288 AC: 11941 AN: 41504

American (AMR) AF: 0.365 AC: 5585 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1716 AN: 3468

East Asian (EAS) AF: 0.561 AC: 2901 AN: 5168

South Asian (SAS) AF: 0.329 AC: 1586 AN: 4828

European-Finnish (FIN) AF: 0.379 AC: 3999 AN: 10560

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28983 AN: 67990

Other (OTH) AF: 0.412 AC: 870 AN: 2110

Alfa AF: 0.397 Hom.: 1498

Bravo AF: 0.381

Asia WGS AF: 0.415 AC: 1443 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.48
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs1018190; hg19: chr17-27547226;