chr1-189502601-T-TAA

Position:

• chr1-189502601-T-TAA

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The XR_002958413.2(LOC105371657):​n.483-65710_483-65709dup 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 0.00119 in 107,828 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0012 (0 hom., cov: 31)
• Consequence: LOC105371657 XR_002958413.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

LOC105371657 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371657	XR_002958413.2	n.483-65710_483-65709dup		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00119 AC: 128 AN: 107824 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00430

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00103

Gnomad ASJ AF: 0.000372

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000295

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000383

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00119 AC: 128 AN: 107828 Hom.: 0 Cov.: 31 AF XY: 0.00124 AC XY: 64 AN XY: 51752

Gnomad4 AFR AF: 0.00429

Gnomad4 AMR AF: 0.00102

Gnomad4 ASJ AF: 0.000372

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000296

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000383

Gnomad4 OTH AF: 0.00

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: rs35854821; hg19: chr1-189471731;