chr1-189502601-T-TA

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The XR_002958413.2(LOC105371657):​n.483-65709dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0262 in 107,700 control chromosomes in the GnomAD database, including 79 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.026 (79 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: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0897 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0262 AC: 2825 AN: 107696 Hom.: 79 Cov.: 31

Gnomad AFR AF: 0.0929

Gnomad AMI AF: 0.00261

Gnomad AMR AF: 0.00970

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.00256

Gnomad SAS AF: 0.0103

Gnomad FIN AF: 0.00115

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00337

Gnomad OTH AF: 0.0181

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

GnomAD4 genome AF: 0.0262 AC: 2825 AN: 107700 Hom.: 79 Cov.: 31 AF XY: 0.0251 AC XY: 1300 AN XY: 51692

African (AFR) AF: 0.0928 AC: 2437 AN: 26268

American (AMR) AF: 0.00969 AC: 104 AN: 10738

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 27 AN: 2682

East Asian (EAS) AF: 0.00257 AC: 10 AN: 3886

South Asian (SAS) AF: 0.0104 AC: 35 AN: 3376

European-Finnish (FIN) AF: 0.00115 AC: 7 AN: 6102

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 188

European-Non Finnish (NFE) AF: 0.00337 AC: 176 AN: 52200

Other (OTH) AF: 0.0181 AC: 27 AN: 1494

Alfa AF: 0.000381 Hom.: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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;