rs11739214

Variant names:

• chr5-180598674-C-G
• rs11739214

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 0.336 in 152,106 control chromosomes in the GnomAD database, including 8,990 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 0.34 (8990 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51075 AN: 151988 Hom.: 8974 Cov.: 32

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.336 AC: 51109 AN: 152106 Hom.: 8990 Cov.: 32 AF XY: 0.338 AC XY: 25118 AN XY: 74344

African (AFR) AF: 0.419 AC: 17407 AN: 41506

American (AMR) AF: 0.262 AC: 4007 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1243 AN: 3468

East Asian (EAS) AF: 0.498 AC: 2561 AN: 5146

South Asian (SAS) AF: 0.339 AC: 1629 AN: 4802

European-Finnish (FIN) AF: 0.282 AC: 2986 AN: 10606

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20234 AN: 67966

Other (OTH) AF: 0.366 AC: 774 AN: 2114

Alfa AF: 0.324 Hom.: 1021

Bravo AF: 0.336

Asia WGS AF: 0.404 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.33
PhyloP100		0.033

Splicing

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

Other links and lift over

dbSNP: rs11739214; hg19: chr5-180025674;