1-1163440-TCC-TC

Variant names:

• chr1-1163440-TC-T
• rs5772039
• XR_007065348.1:n.383-186delC

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The XR_007065348.1(LOC124903818):​n.383-186delC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.88 (59169 hom., cov: 0)
• Consequence: LOC124903818 XR_007065348.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406

Genes affected

LOC124903818 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903818	XR_007065348.1	n.383-186delC		intron_variant	Intron 1 of 1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133322 AN: 151608 Hom.: 59121 Cov.: 0

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.898

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.876

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

GnomAD4 genome AF: 0.879 AC: 133426 AN: 151724 Hom.: 59169 Cov.: 0 AF XY: 0.877 AC XY: 65046 AN XY: 74156

Gnomad4 AFR AF: 0.817

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.900

Gnomad4 NFE AF: 0.930

Gnomad4 OTH AF: 0.877

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5772039; hg19: chr1-1098820;