chr1-189502601-TA-T

Position:

• chr1-189502601-TA-T

Variant summary

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

The XR_002958413.2(LOC105371657):​n.483-65709del 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 0.0024 in 107,786 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0024 (1 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.483-65709del		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00240 AC: 259 AN: 107782 Hom.: 1 Cov.: 31

Gnomad AFR AF: 0.00346

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00158

Gnomad ASJ AF: 0.00261

Gnomad EAS AF: 0.00307

Gnomad SAS AF: 0.00738

Gnomad FIN AF: 0.00197

Gnomad MID AF: 0.0152

Gnomad NFE AF: 0.00167

Gnomad OTH AF: 0.00336

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

GnomAD4 genome AF: 0.00240 AC: 259 AN: 107786 Hom.: 1 Cov.: 31 AF XY: 0.00271 AC XY: 140 AN XY: 51716

Gnomad4 AFR AF: 0.00349

Gnomad4 AMR AF: 0.00158

Gnomad4 ASJ AF: 0.00261

Gnomad4 EAS AF: 0.00309

Gnomad4 SAS AF: 0.00741

Gnomad4 FIN AF: 0.00197

Gnomad4 NFE AF: 0.00167

Gnomad4 OTH AF: 0.00334

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;