1-189502601-TAAAAAAAAAAA-TAAAAAAAAAAAA

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.

Transcripts

RefSeq

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

Ensembl

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

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 v4.3

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;