5-130646510-G-T

Variant names:

• chr5-130646510-G-T
• rs2419065

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 0.429 in 151,896 control chromosomes in the GnomAD database, including 15,556 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 0.43 (15556 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.643 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: 0.428 AC: 65001 AN: 151778 Hom.: 15509 Cov.: 32

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.429 AC: 65111 AN: 151896 Hom.: 15556 Cov.: 32 AF XY: 0.431 AC XY: 32008 AN XY: 74194

African (AFR) AF: 0.650 AC: 26927 AN: 41426

American (AMR) AF: 0.428 AC: 6542 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1231 AN: 3464

East Asian (EAS) AF: 0.446 AC: 2300 AN: 5162

South Asian (SAS) AF: 0.400 AC: 1922 AN: 4800

European-Finnish (FIN) AF: 0.369 AC: 3883 AN: 10512

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21292 AN: 67942

Other (OTH) AF: 0.390 AC: 824 AN: 2112

Alfa AF: 0.381 Hom.: 2391

Bravo AF: 0.443

Asia WGS AF: 0.474 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.22
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2419065; hg19: chr5-129982203;