rs1557054

Variant names:

• chrX-35614660-C-T
• rs1557054
• ENST00000810356.1:n.132G>A

Variant summary

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

The ENST00000810356.1(ENSG00000305308):​n.132G>A variant causes a non coding transcript exon 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 0.56 (12751 hom., 18086 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000305308 ENST00000810356.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 1 publications found

Genes affected

ENSG00000305308 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305308	ENST00000810356.1	n.132G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.565 AC: 61658 AN: 109114 Hom.: 12760 Cov.: 22

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.572

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: 0.565 AC: 61668 AN: 109167 Hom.: 12751 Cov.: 22 AF XY: 0.564 AC XY: 18086 AN XY: 32043

African (AFR) AF: 0.585 AC: 17112 AN: 29243

American (AMR) AF: 0.598 AC: 6150 AN: 10279

Ashkenazi Jewish (ASJ) AF: 0.625 AC: 1644 AN: 2629

East Asian (EAS) AF: 0.718 AC: 2486 AN: 3464

South Asian (SAS) AF: 0.575 AC: 1505 AN: 2617

European-Finnish (FIN) AF: 0.510 AC: 2940 AN: 5764

Middle Eastern (MID) AF: 0.624 AC: 131 AN: 210

European-Non Finnish (NFE) AF: 0.538 AC: 28407 AN: 52808

Other (OTH) AF: 0.575 AC: 855 AN: 1487

Alfa AF: 0.551 Hom.: 4558

Bravo AF: 0.578

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.1
DANN	Benign	0.64
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1557054; hg19: chrX-35632777;