X-37043316-C-A

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_171164.1(FTHL18P):​n.477G>T 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 0.00000894 in 111,862 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

• Frequency:
  • Genomes: 𝑓 0.0000089 (0 hom., 0 hem., cov: 23)
  • Exomes 𝑓: 0.0000023 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: FTHL18P NR_171164.1 non_coding_transcript_exon
• Clinical Significance: Uncertain significance no assertion criteria provided U:2
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).

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>T		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>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000300177	ENST00000769755.1		n.114C>A		non_coding_transcript_exon	Exon 1 of 2
	FTHL18P	ENST00000769915.1		n.477G>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.00000894 AC: 1 AN: 111807 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00422

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000226 AC: 2 AN: 884925 Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0 AN XY: 264747

African (AFR) AF: 0.00 AC: 0 AN: 19307

American (AMR) AF: 0.00 AC: 0 AN: 20410

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 10989

East Asian (EAS) AF: 0.00 AC: 0 AN: 15453

South Asian (SAS) AF: 0.00 AC: 0 AN: 31355

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 22838

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2150

European-Non Finnish (NFE) AF: 0.00000275 AC: 2 AN: 727619

Other (OTH) AF: 0.00 AC: 0 AN: 34804

GnomAD4 genome AF: 0.00000894 AC: 1 AN: 111862 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 34088

African (AFR) AF: 0.00 AC: 0 AN: 30616

American (AMR) AF: 0.00 AC: 0 AN: 10698

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2650

East Asian (EAS) AF: 0.00 AC: 0 AN: 3543

South Asian (SAS) AF: 0.00 AC: 0 AN: 2700

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6133

Middle Eastern (MID) AF: 0.00463 AC: 1 AN: 216

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 53101

Other (OTH) AF: 0.00 AC: 0 AN: 1529

Alfa AF: 0.00 Hom.: 265

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	2	-	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	0.39
DANN	Benign	0.63
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;