rs1419141

Positions:

• chr10-117934993-G-A
• chr10-117934993-G-C
• chr10-117934993-G-T

Variant summary

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

The XR_946348.3(LOC105378504):​n.1735C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 152,008 control chromosomes in the GnomAD database, including 34,701 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 0.67 (34701 hom., cov: 32)
• Consequence: LOC105378504 XR_946348.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0580

Genes affected

LOC105378504 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378504	XR_946348.3	n.1735C>T		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102460 AN: 151890 Hom.: 34652 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.675 AC: 102558 AN: 152008 Hom.: 34701 Cov.: 32 AF XY: 0.675 AC XY: 50187 AN XY: 74308

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.703

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.679

Alfa AF: 0.647 Hom.: 60345

Bravo AF: 0.674

Asia WGS AF: 0.764 AC: 2654 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.57
DANN	Benign	0.12

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1419141; hg19: chr10-119694504;