chrX-148052347-G-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FTH1P8		n.148052347G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FTH1P8	ENST00000498161.1	n.115G>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

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 v4.3

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

Other links and lift over

dbSNP: rs5904861; hg19: chrX-147133867;