rs5904861

Positions:

• chrX-148052347-G-T

Variant summary

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

The ENST00000498161.1(FTH1P8):​n.115G>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0345 in 1,176,807 control chromosomes in the GnomAD database, including 631 homozygotes. There are 12,111 hemizygotes in GnomAD. 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 0.050 (145 hom., 1539 hem., cov: 22)
  • Exomes 𝑓: 0.033 (486 hom. 10572 hem.)
• Consequence: FTH1P8 ENST00000498161.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.06

Genes affected

FTH1P8 (HGNC:3995): (ferritin heavy chain 1 pseudogene 8)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0985 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
FTH1P8	ENST00000498161.1	n.115G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0502 AC: 5621 AN: 112036 Hom.: 145 Cov.: 22 AF XY: 0.0449 AC XY: 1535 AN XY: 34208

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.00146

Gnomad AMR AF: 0.0327

Gnomad ASJ AF: 0.0212

Gnomad EAS AF: 0.00112

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.0420

Gnomad NFE AF: 0.0350

Gnomad OTH AF: 0.0504

GnomAD4 exome AF: 0.0329 AC: 34979 AN: 1064716 Hom.: 486 Cov.: 28 AF XY: 0.0309 AC XY: 10572 AN XY: 342378

Gnomad4 AFR exome AF: 0.102

Gnomad4 AMR exome AF: 0.0196

Gnomad4 ASJ exome AF: 0.0224

Gnomad4 EAS exome AF: 0.000930

Gnomad4 SAS exome AF: 0.0265

Gnomad4 FIN exome AF: 0.0168

Gnomad4 NFE exome AF: 0.0336

Gnomad4 OTH exome AF: 0.0347

GnomAD4 genome AF: 0.0502 AC: 5623 AN: 112091 Hom.: 145 Cov.: 22 AF XY: 0.0449 AC XY: 1539 AN XY: 34273

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0327

Gnomad4 ASJ AF: 0.0212

Gnomad4 EAS AF: 0.00112

Gnomad4 SAS AF: 0.0229

Gnomad4 FIN AF: 0.0133

Gnomad4 NFE AF: 0.0350

Gnomad4 OTH AF: 0.0511

Alfa AF: 0.0432 Hom.: 226

Bravo AF: 0.0538

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	7.7
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5904861; hg19: chrX-147133867;