rs12198581

Variant names:

• chr6-110587889-C-A
• rs12198581
• XR_942865.3:n.386-990C>A

Variant summary

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

The XR_942865.3(LOC105377941):​n.386-990C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,166 control chromosomes in the GnomAD database, including 1,103 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 0.10 (1103 hom., cov: 33)
• Consequence: LOC105377941 XR_942865.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.494
• Publications: 3 publications found

Genes affected

LOC105377941 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 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: 0.102 AC: 15577 AN: 152048 Hom.: 1106 Cov.: 33

Gnomad AFR AF: 0.0250

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0719

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.0908

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.102 AC: 15567 AN: 152166 Hom.: 1103 Cov.: 33 AF XY: 0.103 AC XY: 7638 AN XY: 74398

African (AFR) AF: 0.0249 AC: 1035 AN: 41520

American (AMR) AF: 0.0719 AC: 1099 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 418 AN: 3470

East Asian (EAS) AF: 0.274 AC: 1415 AN: 5166

South Asian (SAS) AF: 0.251 AC: 1213 AN: 4824

European-Finnish (FIN) AF: 0.0908 AC: 962 AN: 10594

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9089 AN: 67982

Other (OTH) AF: 0.107 AC: 225 AN: 2112

Alfa AF: 0.119 Hom.: 595

Bravo AF: 0.0931

Asia WGS AF: 0.228 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.2
DANN	Benign	0.55
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs12198581; hg19: chr6-110909092;