rs1538185

Variant names:

• chr6-129946608-G-A
• rs1538185
• XR_942986.3:n.779-786G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_942986.3(LOC105377999):​n.779-786G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,106 control chromosomes in the GnomAD database, including 2,835 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 0.18 (2835 hom., cov: 32)
• Consequence: LOC105377999 XR_942986.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 4 publications found

Genes affected

LOC105377999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 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: 0.183 AC: 27749 AN: 151988 Hom.: 2833 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.182 AC: 27743 AN: 152106 Hom.: 2835 Cov.: 32 AF XY: 0.186 AC XY: 13822 AN XY: 74344

African (AFR) AF: 0.113 AC: 4711 AN: 41526

American (AMR) AF: 0.194 AC: 2957 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 514 AN: 3468

East Asian (EAS) AF: 0.262 AC: 1355 AN: 5172

South Asian (SAS) AF: 0.157 AC: 757 AN: 4812

European-Finnish (FIN) AF: 0.279 AC: 2942 AN: 10546

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13815 AN: 67986

Other (OTH) AF: 0.191 AC: 403 AN: 2112

Alfa AF: 0.195 Hom.: 12986

Bravo AF: 0.175

Asia WGS AF: 0.191 AC: 663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.1
DANN	Benign	0.79
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs1538185; hg19: chr6-130267753;