rs1186930

Variant names:

• chr5-157864405-A-G
• rs1186930

Your query was ambiguous. Multiple possible variants found:

• chr5-157864405-A-G
• chr5-157864405-A-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 0.593 in 151,634 control chromosomes in the GnomAD database, including 27,395 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 0.59 (27395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 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: 0.593 AC: 89789 AN: 151518 Hom.: 27352 Cov.: 32

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.593 AC: 89882 AN: 151634 Hom.: 27395 Cov.: 32 AF XY: 0.595 AC XY: 44067 AN XY: 74096

African (AFR) AF: 0.675 AC: 27696 AN: 41036

American (AMR) AF: 0.465 AC: 7113 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2147 AN: 3470

East Asian (EAS) AF: 0.395 AC: 2037 AN: 5152

South Asian (SAS) AF: 0.600 AC: 2894 AN: 4822

European-Finnish (FIN) AF: 0.676 AC: 7155 AN: 10586

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 38995 AN: 67970

Other (OTH) AF: 0.583 AC: 1230 AN: 2110

Alfa AF: 0.600 Hom.: 3557

Bravo AF: 0.574

Asia WGS AF: 0.501 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.70
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs1186930; hg19: chr5-157291413;