2-127133887-T-TGGGG

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The XR_923311.4(LOC105373605):n.910+587_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 0.0025 (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 Likely_benign. Variant got -4 ACMG points.

• 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+587_910+590dup		intron_variant, non_coding_transcript_variant
LOC105373605	XR_923310.3	n.513+587_513+590dup		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.00247 AC: 374 AN: 151116 Hom.: 3 Cov.: 0

Gnomad AFR AF: 0.00341

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00573

Gnomad ASJ AF: 0.00173

Gnomad EAS AF: 0.00194

Gnomad SAS AF: 0.00375

Gnomad FIN AF: 0.000479

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00152

Gnomad OTH AF: 0.00242

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

GnomAD4 genome AF: 0.00253 AC: 382 AN: 151234 Hom.: 4 Cov.: 0 AF XY: 0.00269 AC XY: 199 AN XY: 73882

Gnomad4 AFR AF: 0.00357

Gnomad4 AMR AF: 0.00585

Gnomad4 ASJ AF: 0.00173

Gnomad4 EAS AF: 0.00195

Gnomad4 SAS AF: 0.00354

Gnomad4 FIN AF: 0.000479

Gnomad4 NFE AF: 0.00152

Gnomad4 OTH AF: 0.00239

Alfa AF: 0.000395 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;