XR_001749352.3:n.328-1226G>A

Variant names:

• chr12-121128067-C-T
• rs9805004
• XR_001749352.3:n.328-1226G>A

Variant summary

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

The XR_001749352.3(LOC105370032):​n.328-1226G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0991 in 152,196 control chromosomes in the GnomAD database, including 806 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 0.099 (806 hom., cov: 31)
• Consequence: LOC105370032 XR_001749352.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 6 publications found

Genes affected

LOC105370032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.149 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: 0.0991 AC: 15072 AN: 152078 Hom.: 803 Cov.: 31

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0816

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0991 AC: 15085 AN: 152196 Hom.: 806 Cov.: 31 AF XY: 0.0976 AC XY: 7260 AN XY: 74422

African (AFR) AF: 0.0747 AC: 3103 AN: 41530

American (AMR) AF: 0.0956 AC: 1461 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0701 AC: 243 AN: 3468

East Asian (EAS) AF: 0.115 AC: 596 AN: 5176

South Asian (SAS) AF: 0.159 AC: 765 AN: 4818

European-Finnish (FIN) AF: 0.0816 AC: 865 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7650 AN: 67992

Other (OTH) AF: 0.108 AC: 228 AN: 2112

Alfa AF: 0.106 Hom.: 706

Bravo AF: 0.0969

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.73
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs9805004; hg19: chr12-121565870;