XR_001740941.2:n.19987+5947T>C

Variant names:

• chr3-144245214-T-C
• rs10513240
• XR_001740941.2:n.19987+5947T>C

Variant summary

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

The XR_001740941.2(LOC105374140):​n.19987+5947T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0588 in 151,956 control chromosomes in the GnomAD database, including 373 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 0.059 (373 hom., cov: 32)
• Consequence: LOC105374140 XR_001740941.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 1 publications found

Genes affected

LOC105374140 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 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: 0.0588 AC: 8922 AN: 151838 Hom.: 371 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0740

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0948

Gnomad FIN AF: 0.0279

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0378

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0588 AC: 8931 AN: 151956 Hom.: 373 Cov.: 32 AF XY: 0.0600 AC XY: 4454 AN XY: 74258

African (AFR) AF: 0.0772 AC: 3203 AN: 41488

American (AMR) AF: 0.0744 AC: 1135 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0779 AC: 270 AN: 3466

East Asian (EAS) AF: 0.166 AC: 846 AN: 5108

South Asian (SAS) AF: 0.0946 AC: 455 AN: 4808

European-Finnish (FIN) AF: 0.0279 AC: 296 AN: 10606

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

European-Non Finnish (NFE) AF: 0.0378 AC: 2564 AN: 67908

Other (OTH) AF: 0.0616 AC: 130 AN: 2112

Alfa AF: 0.0517 Hom.: 40

Bravo AF: 0.0627

Asia WGS AF: 0.151 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.69
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10513240; hg19: chr3-143964056;