chr5-172771284-GT-G

Position:

• chr5-172771284-GT-G

Variant summary

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

The variant allele was found at a frequency of 0.38 in 200,342 control chromosomes in the GnomAD database, including 16,408 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.37 (11849 hom., cov: 0)
  • Exomes 𝑓: 0.40 (4559 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.855

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.172771285delT		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000253736	ENST00000523005.1	n.70-6207delT		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56659 AN: 151232 Hom.: 11848 Cov.: 0

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.402

GnomAD4 exome AF: 0.397 AC: 19434 AN: 49000 Hom.: 4559 AF XY: 0.405 AC XY: 10080 AN XY: 24880

Gnomad4 AFR exome AF: 0.149

Gnomad4 AMR exome AF: 0.357

Gnomad4 ASJ exome AF: 0.410

Gnomad4 EAS exome AF: 0.215

Gnomad4 SAS exome AF: 0.361

Gnomad4 FIN exome AF: 0.412

Gnomad4 NFE exome AF: 0.439

Gnomad4 OTH exome AF: 0.391

GnomAD4 genome AF: 0.374 AC: 56668 AN: 151342 Hom.: 11849 Cov.: 0 AF XY: 0.373 AC XY: 27572 AN XY: 73928

Gnomad4 AFR AF: 0.181

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.467

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.396

Bravo AF: 0.362

Asia WGS AF: 0.298 AC: 1036 AN: 3458

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: rs28372789; hg19: chr5-172198287;