rs12760731

Variant names:

• chr1-178502087-C-T
• rs12760731
• XR_001738305.2:n.1269-546G>A

Variant summary

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

The XR_001738305.2(LOC101928866):​n.1269-546G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,244 control chromosomes in the GnomAD database, including 1,220 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 0.12 (1220 hom., cov: 33)
• Consequence: LOC101928866 XR_001738305.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.397
• Publications: 6 publications found

Genes affected

LOC101928866 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 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: 0.116 AC: 17634 AN: 152126 Hom.: 1209 Cov.: 33

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0794

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.0547

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.0627

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.0987

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.116 AC: 17681 AN: 152244 Hom.: 1220 Cov.: 33 AF XY: 0.112 AC XY: 8344 AN XY: 74436

African (AFR) AF: 0.193 AC: 8020 AN: 41522

American (AMR) AF: 0.0791 AC: 1211 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3470

East Asian (EAS) AF: 0.0544 AC: 282 AN: 5180

South Asian (SAS) AF: 0.0504 AC: 243 AN: 4824

European-Finnish (FIN) AF: 0.0627 AC: 665 AN: 10608

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0987 AC: 6710 AN: 68010

Other (OTH) AF: 0.116 AC: 245 AN: 2114

Alfa AF: 0.107 Hom.: 627

Bravo AF: 0.119

Asia WGS AF: 0.117 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.59
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs12760731; hg19: chr1-178471222;