rs1506030

Variant names:

• chr5-10055804-G-A
• rs1506030

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 0.473 in 152,066 control chromosomes in the GnomAD database, including 18,139 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 0.47 (18139 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.565 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: 0.473 AC: 71895 AN: 151948 Hom.: 18141 Cov.: 33

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.473 AC: 71903 AN: 152066 Hom.: 18139 Cov.: 33 AF XY: 0.468 AC XY: 34780 AN XY: 74322

African (AFR) AF: 0.319 AC: 13204 AN: 41440

American (AMR) AF: 0.492 AC: 7523 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1939 AN: 3472

East Asian (EAS) AF: 0.203 AC: 1052 AN: 5186

South Asian (SAS) AF: 0.433 AC: 2089 AN: 4828

European-Finnish (FIN) AF: 0.533 AC: 5623 AN: 10542

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.570 AC: 38733 AN: 67990

Other (OTH) AF: 0.497 AC: 1048 AN: 2108

Alfa AF: 0.535 Hom.: 99193

Bravo AF: 0.463

Asia WGS AF: 0.307 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.4
DANN	Benign	0.33
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1506030; hg19: chr5-10055916;