X-112403236-C-T

Variant names:

• chrX-112403236-C-T
• rs5982533
• NM_001395362.2:c.-284-27878C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001395362.2(RTL4):​c.-284-27878C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.63 (16608 hom., 20673 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: RTL4 NM_001395362.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343
• Publications: 5 publications found

Genes affected

RTL4 (HGNC:25214): (retrotransposon Gag like 4) Predicted to enable nucleic acid binding activity and zinc ion binding activity. Predicted to act upstream of or within cognition and norepinephrine metabolic process. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RTL4	NM_001395362.2	c.-284-27878C>T		intron_variant	Intron 3 of 4	ENST00000695839.1	NP_001382291.1
RTL4	NM_001004308.3	c.-229-51264C>T		intron_variant	Intron 2 of 2		NP_001004308.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RTL4	ENST00000695839.1	c.-284-27878C>T		intron_variant	Intron 3 of 4		NM_001395362.2	ENSP00000512211.1
RTL4	ENST00000340433.4	c.-284-27878C>T		intron_variant	Intron 2 of 3	6		ENSP00000340590.2
RTL4	ENST00000695808.1	c.-229-51264C>T		intron_variant	Intron 2 of 2			ENSP00000512188.1

Frequencies

GnomAD3 genomes AF: 0.633 AC: 69901 AN: 110386 Hom.: 16618 Cov.: 22

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.660

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.633 AC: 69891 AN: 110437 Hom.: 16608 Cov.: 22 AF XY: 0.632 AC XY: 20673 AN XY: 32705

African (AFR) AF: 0.389 AC: 11830 AN: 30421

American (AMR) AF: 0.680 AC: 7070 AN: 10391

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2093 AN: 2623

East Asian (EAS) AF: 0.640 AC: 2222 AN: 3471

South Asian (SAS) AF: 0.629 AC: 1632 AN: 2593

European-Finnish (FIN) AF: 0.714 AC: 4122 AN: 5777

Middle Eastern (MID) AF: 0.684 AC: 147 AN: 215

European-Non Finnish (NFE) AF: 0.744 AC: 39233 AN: 52762

Other (OTH) AF: 0.654 AC: 986 AN: 1508

Alfa AF: 0.701 Hom.: 71423

Bravo AF: 0.623

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.80
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs5982533; hg19: chrX-111646464;