6-1290153-C-T

Variant names:

• chr6-1290153-C-T
• rs10793833
• XR_001743918.2:n.4349G>A

Variant summary

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

The XR_001743918.2(LOC105374879):​n.4349G>A 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 0.74 in 151,968 control chromosomes in the GnomAD database, including 41,979 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 0.74 (41979 hom., cov: 31)
• Consequence: LOC105374879 XR_001743918.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.756

Genes affected

LOC105374879 (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 (NFE) allele frequency at 95% confidence interval = 0.771 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374879	XR_001743918.2	n.4349G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112285 AN: 151850 Hom.: 41944 Cov.: 31

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.776

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.740 AC: 112387 AN: 151968 Hom.: 41979 Cov.: 31 AF XY: 0.741 AC XY: 55025 AN XY: 74288

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.793

Gnomad4 EAS AF: 0.490

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.776

Gnomad4 OTH AF: 0.753

Alfa AF: 0.762 Hom.: 11348

Bravo AF: 0.731

Asia WGS AF: 0.602 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.35
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10793833; hg19: chr6-1290388;