rs10513240

Positions:

• chr3-144245214-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007096124.1(LOC105374140):​n.19987+5947T>C variant causes a intron, non coding transcript 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_007096124.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

Genes affected

LOC105374140 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105374140	XR_007096124.1	n.19987+5947T>C		intron_variant, non_coding_transcript_variant
LOC105374140	XR_001740941.2	n.19987+5947T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0772

Gnomad4 AMR AF: 0.0744

Gnomad4 ASJ AF: 0.0779

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.0946

Gnomad4 FIN AF: 0.0279

Gnomad4 NFE AF: 0.0378

Gnomad4 OTH AF: 0.0616

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513240; hg19: chr3-143964056;