chrX-71181867-A-T

Variant names:

• chrX-71181867-A-T
• rs5981084
• ENST00000740246.1:n.346+2044T>A

Variant summary

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

The ENST00000740246.1(ENSG00000228427):​n.346+2044T>A 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 0.91 (32351 hom., 29801 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000228427 ENST00000740246.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.248
• Publications: 0 publications found

Genes affected

ENSG00000228427 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000740246.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228427	ENST00000740246.1		n.346+2044T>A		intron	N/A
	ENSG00000228427	ENST00000740247.1		n.367+2044T>A		intron	N/A
	ENSG00000228427	ENST00000740248.1		n.212+13T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.910 AC: 100549 AN: 110484 Hom.: 32351 Cov.: 22

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.924

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.932

Gnomad NFE AF: 0.867

Gnomad OTH AF: 0.923

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: 0.910 AC: 100608 AN: 110537 Hom.: 32351 Cov.: 22 AF XY: 0.910 AC XY: 29801 AN XY: 32737

African (AFR) AF: 0.982 AC: 29876 AN: 30438

American (AMR) AF: 0.928 AC: 9690 AN: 10441

Ashkenazi Jewish (ASJ) AF: 0.924 AC: 2441 AN: 2641

East Asian (EAS) AF: 0.999 AC: 3447 AN: 3449

South Asian (SAS) AF: 0.987 AC: 2559 AN: 2592

European-Finnish (FIN) AF: 0.806 AC: 4663 AN: 5788

Middle Eastern (MID) AF: 0.949 AC: 203 AN: 214

European-Non Finnish (NFE) AF: 0.867 AC: 45777 AN: 52799

Other (OTH) AF: 0.924 AC: 1393 AN: 1507

Alfa AF: 0.897 Hom.: 7926

Bravo AF: 0.921

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.6
DANN	Benign	0.82
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs5981084; hg19: chrX-70401717;