rs59335482

chr2-127133887-T-TGchr2-127133887-T-TGGchr2-127133887-T-TGGGchr2-127133887-T-TGGGGchr2-127133887-T-TGGGGGchr2-127133887-T-TGGGGGG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The XR_923311.4(LOC105373605):n.910+590dup variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.0053 (4 hom., cov: 0)
• Consequence: LOC105373605 XR_923311.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396

Genes affected

LOC105373605 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00534 (807/151232) while in subpopulation AFR AF= 0.0172 (707/41120). AF 95% confidence interval is 0.0161. There are 4 homozygotes in gnomad4. There are 373 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373605	XR_923311.4	n.910+590dup		intron_variant, non_coding_transcript_variant
LOC105373605	XR_923310.3	n.513+590dup		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00531 AC: 803 AN: 151114 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.0171

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00191

Gnomad ASJ AF: 0.000289

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.000192

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.000797

Gnomad OTH AF: 0.00484

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

GnomAD4 genome AF: 0.00534 AC: 807 AN: 151232 Hom.: 4 Cov.: 0 AF XY: 0.00505 AC XY: 373 AN XY: 73882

Gnomad4 AFR AF: 0.0172

Gnomad4 AMR AF: 0.00191

Gnomad4 ASJ AF: 0.000289

Gnomad4 EAS AF: 0.000195

Gnomad4 SAS AF: 0.000208

Gnomad4 FIN AF: 0.000192

Gnomad4 NFE AF: 0.000797

Gnomad4 OTH AF: 0.00478

Alfa AF: 0.000593 Hom.: 194

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: rs59335482; hg19: chr2-127891463;