XR_002958413.2:n.483-65709delA

Variant names:

• chr1-189502601-TA-T
• rs35854821
• XR_002958413.2:n.483-65709delA

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The XR_002958413.2(LOC105371657):​n.483-65709delA variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 0 publications found

Genes affected

LOC105371657 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371657	XR_002958413.2	n.483-65709delA		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.00349 AC: 92 AN: 26338

American (AMR) AF: 0.00158 AC: 17 AN: 10742

Ashkenazi Jewish (ASJ) AF: 0.00261 AC: 7 AN: 2686

East Asian (EAS) AF: 0.00309 AC: 12 AN: 3884

South Asian (SAS) AF: 0.00741 AC: 25 AN: 3374

European-Finnish (FIN) AF: 0.00197 AC: 12 AN: 6098

Middle Eastern (MID) AF: 0.0106 AC: 2 AN: 188

European-Non Finnish (NFE) AF: 0.00167 AC: 87 AN: 52214

Other (OTH) AF: 0.00334 AC: 5 AN: 1496

Alfa AF: 0.00 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs35854821; hg19: chr1-189471731; COSMIC: COSV66172302;