rs11739135

Variant names:

• chr5-132397705-G-C
• rs11739135

Your query was ambiguous. Multiple possible variants found:

• chr5-132397705-G-C
• chr5-132397705-G-T

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 0.272 in 152,170 control chromosomes in the GnomAD database, including 7,272 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 (7272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.394 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: 0.273 AC: 41455 AN: 152052 Hom.: 7275 Cov.: 32

Gnomad AFR AF: 0.0881

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.272 AC: 41446 AN: 152170 Hom.: 7272 Cov.: 32 AF XY: 0.261 AC XY: 19449 AN XY: 74394

African (AFR) AF: 0.0879 AC: 3652 AN: 41540

American (AMR) AF: 0.297 AC: 4536 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5180

South Asian (SAS) AF: 0.106 AC: 509 AN: 4822

European-Finnish (FIN) AF: 0.282 AC: 2987 AN: 10584

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27085 AN: 67972

Other (OTH) AF: 0.318 AC: 671 AN: 2110

Alfa AF: 0.212 Hom.: 535

Bravo AF: 0.270

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.77
DANN	Benign	0.51
PhyloP100		0.035

Splicing

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

Other links and lift over

dbSNP: rs11739135; hg19: chr5-131733397; COSMIC: COSV55375179;