rs17639207

Variant names:

• chr4-135272185-T-C
• rs17639207

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 0.248 in 151,200 control chromosomes in the GnomAD database, including 5,165 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 0.25 (5165 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37478 AN: 151086 Hom.: 5158 Cov.: 29

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.248 AC: 37508 AN: 151200 Hom.: 5165 Cov.: 29 AF XY: 0.248 AC XY: 18288 AN XY: 73744

African (AFR) AF: 0.147 AC: 6043 AN: 41236

American (AMR) AF: 0.322 AC: 4866 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1078 AN: 3468

East Asian (EAS) AF: 0.139 AC: 716 AN: 5138

South Asian (SAS) AF: 0.371 AC: 1773 AN: 4782

European-Finnish (FIN) AF: 0.230 AC: 2364 AN: 10300

Middle Eastern (MID) AF: 0.372 AC: 108 AN: 290

European-Non Finnish (NFE) AF: 0.290 AC: 19649 AN: 67864

Other (OTH) AF: 0.298 AC: 624 AN: 2092

Alfa AF: 0.251 Hom.: 621

Bravo AF: 0.250

Asia WGS AF: 0.281 AC: 977 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.65
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs17639207; hg19: chr4-136193340;