Genetic Variant ENST00000412071.1:n.255C>T (chrX-37043317-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000412071.1(FTHL18P):n.255C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0000863 in 1,008,231 control chromosomes in the GnomAD database, including 2 homozygotes. There are 41 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000089 ( 0 hom., 5 hem., cov: 24)

Exomes 𝑓: 0.000086 ( 2 hom. 36 hem. )

Consequence

FTHL18P
ENST00000412071.1 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 6.32

Publications

0 publications found

Variant links:

Genes affected

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

FTHL18P links:

ENSG00000300177 (HGNC:):

ENSG00000300177 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.47).

BP6

Variant X-37043317-G-A is Benign according to our data. Variant chrX-37043317-G-A is described in ClinVar as Likely_benign. ClinVar VariationId is 2660277.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 5 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412071.1. 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.476C>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
FTHL18P	ENST00000412071.1	TSL:6	n.255C>T	non_coding_transcript_exon	Exon 1 of 1
ENSG00000300177	ENST00000769755.1		n.115G>A	non_coding_transcript_exon	Exon 1 of 2
FTHL18P	ENST00000769915.1		n.476C>T	non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0000888

AC:

AN:

112602

Hom.:

Cov.:

show subpopulations

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:

0.00221

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000751

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000860

AC:

AN:

895629

Hom.:

Cov.:

AF XY:

0.000134

AC XY:

AN XY:

268537

show subpopulations

African (AFR)

AF:

0.0000506

AC:

AN:

19750

American (AMR)

AF:

0.0000466

AC:

AN:

21447

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11318

East Asian (EAS)

AF:

0.00

AC:

AN:

15926

South Asian (SAS)

AF:

0.00130

AC:

AN:

32968

European-Finnish (FIN)

AF:

0.00

AC:

AN:

23203

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2188

European-Non Finnish (NFE)

AF:

0.0000368

AC:

AN:

733489

Other (OTH)

AF:

0.000141

AC:

AN:

35340

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000888

AC:

AN:

112602

Hom.:

Cov.:

AF XY:

0.000144

AC XY:

AN XY:

34748

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

30981

American (AMR)

AF:

0.00

AC:

AN:

10745

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2656

East Asian (EAS)

AF:

0.00

AC:

AN:

3575

South Asian (SAS)

AF:

0.00221

AC:

AN:

2711

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6211

Middle Eastern (MID)

AF:

0.00

AC:

AN:

239

European-Non Finnish (NFE)

AF:

0.0000751

AC:

AN:

53278

Other (OTH)

AF:

0.00

AC:

AN:

1523

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.465

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000416

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.47

CADD

Benign

6.2

(source)

DANN

Benign

0.51

PhyloP100

6.3

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over