5-1299744-G-C

Variant names:

• chr5-1299744-G-C
• rs13174814

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 0.26 in 151,790 control chromosomes in the GnomAD database, including 5,411 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 0.26 (5411 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39387 AN: 151672 Hom.: 5409 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.260 AC: 39406 AN: 151790 Hom.: 5411 Cov.: 32 AF XY: 0.264 AC XY: 19602 AN XY: 74172

African (AFR) AF: 0.204 AC: 8446 AN: 41424

American (AMR) AF: 0.339 AC: 5160 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 848 AN: 3466

East Asian (EAS) AF: 0.495 AC: 2529 AN: 5110

South Asian (SAS) AF: 0.267 AC: 1283 AN: 4804

European-Finnish (FIN) AF: 0.308 AC: 3239 AN: 10532

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17208 AN: 67904

Other (OTH) AF: 0.236 AC: 497 AN: 2110

Alfa AF: 0.170 Hom.: 364

Bravo AF: 0.262

Asia WGS AF: 0.378 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.37
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs13174814; hg19: chr5-1299859;