rs1419141

Variant names:

• chr10-117934993-G-A
• rs1419141
• XR_946348.3:n.1735C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

LOC105378504 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.675 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

African (AFR) AF: 0.721 AC: 29883 AN: 41470

American (AMR) AF: 0.667 AC: 10187 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2174 AN: 3468

East Asian (EAS) AF: 0.726 AC: 3746 AN: 5162

South Asian (SAS) AF: 0.703 AC: 3372 AN: 4798

European-Finnish (FIN) AF: 0.671 AC: 7087 AN: 10562

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44041 AN: 67958

Other (OTH) AF: 0.679 AC: 1437 AN: 2116

Alfa AF: 0.652 Hom.: 94200

Bravo AF: 0.674

Asia WGS AF: 0.764 AC: 2654 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.57
DANN	Benign	0.12
PhyloP100		0.058

Splicing

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

Other links and lift over

dbSNP: rs1419141; hg19: chr10-119694504;