rs28362491

chr4-102500997-CATTG-Cchr4-102500997-CATTG-CATTGATTG

Variant summary

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

The ENST00000563833.1(ENSG00000260651):n.319_322del variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 153,546 control chromosomes in the GnomAD database, including 14,272 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.43 (14166 hom., cov: 0)
  • Exomes 𝑓: 0.32 (106 hom.)
• Consequence: ENST00000563833.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377621	NR_136202.1	n.48+1438_48+1441del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000563833.1	n.319_322del		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64938 AN: 151662 Hom.: 14138 Cov.: 0

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.402

GnomAD4 exome AF: 0.323 AC: 570 AN: 1764 Hom.: 106 AF XY: 0.327 AC XY: 353 AN XY: 1080

Gnomad4 AFR exome AF: 0.350

Gnomad4 AMR exome AF: 0.429

Gnomad4 ASJ exome AF: 0.139

Gnomad4 EAS exome AF: 0.313

Gnomad4 SAS exome AF: 0.167

Gnomad4 FIN exome AF: 0.489

Gnomad4 NFE exome AF: 0.331

Gnomad4 OTH exome AF: 0.256

GnomAD4 genome AF: 0.428 AC: 65010 AN: 151782 Hom.: 14166 Cov.: 0 AF XY: 0.429 AC XY: 31815 AN XY: 74188

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.398

Alfa AF: 0.416 Hom.: 1645

Bravo AF: 0.439

Asia WGS AF: 0.354 AC: 1226 AN: 3476

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: rs28362491; hg19: chr4-103422154;