1-189502601-T-TA

Position:

• chr1-189502601-T-TA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.189502601_189502602insA		intergenic_region
LOC105371657	XR_002958413.2	n.483-65709dupA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0928

Gnomad4 AMR AF: 0.00969

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.00257

Gnomad4 SAS AF: 0.0104

Gnomad4 FIN AF: 0.00115

Gnomad4 NFE AF: 0.00337

Gnomad4 OTH AF: 0.0181

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;