rs17590261

Variant names:

• chr4-135642969-T-C
• rs17590261

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 0.195 in 151,986 control chromosomes in the GnomAD database, including 3,251 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 0.19 (3251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 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: 0.195 AC: 29605 AN: 151866 Hom.: 3248 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0479

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.195 AC: 29619 AN: 151986 Hom.: 3251 Cov.: 32 AF XY: 0.191 AC XY: 14217 AN XY: 74290

African (AFR) AF: 0.109 AC: 4528 AN: 41492

American (AMR) AF: 0.190 AC: 2893 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 504 AN: 3470

East Asian (EAS) AF: 0.0477 AC: 246 AN: 5162

South Asian (SAS) AF: 0.139 AC: 669 AN: 4822

European-Finnish (FIN) AF: 0.231 AC: 2437 AN: 10534

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17708 AN: 67956

Other (OTH) AF: 0.170 AC: 357 AN: 2104

Alfa AF: 0.230 Hom.: 4628

Bravo AF: 0.187

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.86
DANN	Benign	0.64
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs17590261; hg19: chr4-136564124;