rs5904861

Variant names:

• chrX-148052347-G-T
• rs5904861
• ENST00000498161.1:n.115G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000498161.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTH1P8	ENST00000498161.1	TSL:6	n.115G>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0502 AC: 5621 AN: 112036 Hom.: 145 Cov.: 22

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

African (AFR) AF: 0.102 AC: 2647 AN: 25875

American (AMR) AF: 0.0196 AC: 690 AN: 35179

Ashkenazi Jewish (ASJ) AF: 0.0224 AC: 432 AN: 19279

East Asian (EAS) AF: 0.000930 AC: 28 AN: 30123

South Asian (SAS) AF: 0.0265 AC: 1419 AN: 53643

European-Finnish (FIN) AF: 0.0168 AC: 497 AN: 29574

Middle Eastern (MID) AF: 0.0265 AC: 91 AN: 3438

European-Non Finnish (NFE) AF: 0.0336 AC: 27602 AN: 822336

Other (OTH) AF: 0.0347 AC: 1573 AN: 45269

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

African (AFR) AF: 0.101 AC: 3123 AN: 30783

American (AMR) AF: 0.0327 AC: 347 AN: 10622

Ashkenazi Jewish (ASJ) AF: 0.0212 AC: 56 AN: 2646

East Asian (EAS) AF: 0.00112 AC: 4 AN: 3571

South Asian (SAS) AF: 0.0229 AC: 61 AN: 2667

European-Finnish (FIN) AF: 0.0133 AC: 82 AN: 6148

Middle Eastern (MID) AF: 0.0413 AC: 9 AN: 218

European-Non Finnish (NFE) AF: 0.0350 AC: 1863 AN: 53242

Other (OTH) AF: 0.0511 AC: 77 AN: 1508

Alfa AF: 0.0432 Hom.: 226

Bravo AF: 0.0538

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	7.7
DANN	Benign	0.71
PhyloP100		7.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5904861;

hg19: chrX-147133867;