chr5-41126148-G-C

Variant names:

• chr5-41126148-G-C
• rs10512762
• XR_001742650.2:n.886+12325G>C

Variant summary

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

The XR_001742650.2(LOC105374739):​n.886+12325G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,142 control chromosomes in the GnomAD database, including 5,816 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 0.25 (5816 hom., cov: 33)
• Consequence: LOC105374739 XR_001742650.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 2 publications found

Genes affected

LOC105374739 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.344 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: 0.252 AC: 38316 AN: 152024 Hom.: 5817 Cov.: 33

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.252 AC: 38308 AN: 152142 Hom.: 5816 Cov.: 33 AF XY: 0.252 AC XY: 18760 AN XY: 74356

African (AFR) AF: 0.0905 AC: 3758 AN: 41538

American (AMR) AF: 0.225 AC: 3444 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3472

East Asian (EAS) AF: 0.118 AC: 611 AN: 5184

South Asian (SAS) AF: 0.213 AC: 1026 AN: 4818

European-Finnish (FIN) AF: 0.384 AC: 4052 AN: 10546

Middle Eastern (MID) AF: 0.228 AC: 66 AN: 290

European-Non Finnish (NFE) AF: 0.348 AC: 23645 AN: 67986

Other (OTH) AF: 0.272 AC: 574 AN: 2108

Alfa AF: 0.208 Hom.: 574

Bravo AF: 0.228

Asia WGS AF: 0.140 AC: 487 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.45
DANN	Benign	0.68
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs10512762; hg19: chr5-41126250;