rs10513240

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374140	XR_001740941.2	n.19987+5947T>C		intron_variant	Intron 2 of 4
LOC105374140	XR_007096124.1	n.19987+5947T>C		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;