X-37043316-C-T

Variant names:

• chrX-37043316-C-T
• rs28675922
• ENST00000412071.1:n.256G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_171164.1(FTHL18P):​n.477G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 996,071 control chromosomes in the GnomAD database, including 12,422 homozygotes. There are 39,226 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 0.27 (5313 hom., 8750 hem., cov: 23)
  • Exomes 𝑓: 0.12 (7109 hom. 30476 hem.)
• Consequence: FTHL18P NR_171164.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.707
• Publications: 4 publications found

Genes affected

FTHL18P (HGNC:3988): (ferritin heavy chain like 18, pseudogene)

ENSG00000300177 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_171164.1. 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
	FTHL18P	NR_171164.1		n.477G>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTHL18P	ENST00000412071.1	TSL:6	n.256G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000300177	ENST00000769755.1		n.114C>T		non_coding_transcript_exon	Exon 1 of 2
	FTHL18P	ENST00000769915.1		n.477G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.271 AC: 30317 AN: 111776 Hom.: 5302 Cov.: 23

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.0858

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.252

GnomAD4 exome AF: 0.118 AC: 104129 AN: 884242 Hom.: 7109 Cov.: 29 AF XY: 0.115 AC XY: 30476 AN XY: 264608

African (AFR) AF: 0.674 AC: 12989 AN: 19281

American (AMR) AF: 0.213 AC: 4327 AN: 20292

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 1428 AN: 10963

East Asian (EAS) AF: 0.0760 AC: 1171 AN: 15413

South Asian (SAS) AF: 0.134 AC: 4202 AN: 31282

European-Finnish (FIN) AF: 0.124 AC: 2835 AN: 22817

Middle Eastern (MID) AF: 0.179 AC: 385 AN: 2150

European-Non Finnish (NFE) AF: 0.0984 AC: 71530 AN: 727288

Other (OTH) AF: 0.151 AC: 5262 AN: 34756

GnomAD4 genome AF: 0.272 AC: 30379 AN: 111829 Hom.: 5313 Cov.: 23 AF XY: 0.257 AC XY: 8750 AN XY: 34067

African (AFR) AF: 0.654 AC: 20025 AN: 30599

American (AMR) AF: 0.246 AC: 2626 AN: 10692

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 341 AN: 2650

East Asian (EAS) AF: 0.0895 AC: 317 AN: 3543

South Asian (SAS) AF: 0.145 AC: 391 AN: 2699

European-Finnish (FIN) AF: 0.112 AC: 686 AN: 6129

Middle Eastern (MID) AF: 0.153 AC: 33 AN: 215

European-Non Finnish (NFE) AF: 0.104 AC: 5510 AN: 53097

Other (OTH) AF: 0.256 AC: 392 AN: 1529

Alfa AF: 0.0585 Hom.: 265

Bravo AF: 0.298

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	0.49
DANN	Benign	0.69
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs28675922; hg19: chrX-37061389;