XR_945388.3:n.119-9710G>A

Variant names:

• chr12-115518124-C-T
• rs7134205
• XR_945388.3:n.119-9710G>A

Variant summary

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

The XR_945388.3(LOC105370003):​n.119-9710G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,084 control chromosomes in the GnomAD database, including 3,265 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 0.13 (3265 hom., cov: 33)
• Consequence: LOC105370003 XR_945388.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 2 publications found

Genes affected

LOC105370003 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.383 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: 0.133 AC: 20206 AN: 151966 Hom.: 3252 Cov.: 33

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0648

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.00705

Gnomad FIN AF: 0.0355

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0339

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.133 AC: 20261 AN: 152084 Hom.: 3265 Cov.: 33 AF XY: 0.128 AC XY: 9482 AN XY: 74368

African (AFR) AF: 0.388 AC: 16032 AN: 41364

American (AMR) AF: 0.0646 AC: 989 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0755 AC: 262 AN: 3472

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5186

South Asian (SAS) AF: 0.00685 AC: 33 AN: 4820

European-Finnish (FIN) AF: 0.0355 AC: 376 AN: 10606

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0339 AC: 2304 AN: 68016

Other (OTH) AF: 0.104 AC: 220 AN: 2112

Alfa AF: 0.105 Hom.: 320

Bravo AF: 0.148

Asia WGS AF: 0.0320 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.74
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs7134205; hg19: chr12-115955929;