chr17-44364976-T-C

Position:

• chr17-44364976-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 17-44364976-T-C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 692,192 control chromosomes in the GnomAD database, including 54,036 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.39 (11891 hom., cov: 31)
  • Exomes 𝑓: 0.39 (42145 hom.)
• Consequence: RPL7L1P5 ENST00000590816.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226

Genes affected

RPL7L1P5 (HGNC:39487): (RPL7L1 pseudogene 5)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RPL7L1P5	ENST00000590816.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59975 AN: 151752 Hom.: 11896 Cov.: 31

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.370

GnomAD4 exome AF: 0.392 AC: 212054 AN: 540322 Hom.: 42145 Cov.: 6 AF XY: 0.390 AC XY: 113019 AN XY: 289802

Gnomad4 AFR exome AF: 0.380

Gnomad4 AMR exome AF: 0.389

Gnomad4 ASJ exome AF: 0.440

Gnomad4 EAS exome AF: 0.432

Gnomad4 SAS exome AF: 0.351

Gnomad4 FIN exome AF: 0.435

Gnomad4 NFE exome AF: 0.391

Gnomad4 OTH exome AF: 0.391

GnomAD4 genome AF: 0.395 AC: 59981 AN: 151870 Hom.: 11891 Cov.: 31 AF XY: 0.393 AC XY: 29134 AN XY: 74188

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.367

Alfa AF: 0.388 Hom.: 20030

Bravo AF: 0.389

Asia WGS AF: 0.405 AC: 1416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	5.3
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs708382; hg19: chr17-42442344;