rs17267847

Variant names:

• chrX-129643057-C-T
• rs17267847
• ENST00000835927.1:n.581C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000835927.1(ENSG00000308713):​n.581C>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 0.0403 in 112,136 control chromosomes in the GnomAD database, including 86 homozygotes. There are 1,350 hemizygotes in GnomAD. 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 0.040 (86 hom., 1350 hem., cov: 24)
• Consequence: ENSG00000308713 ENST00000835927.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 2 publications found

Genes affected

ENSG00000308713 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835927.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308713	ENST00000835927.1		n.581C>T		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000308713	ENST00000835930.1		n.581C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000308713	ENST00000835926.1		n.241-243C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0404 AC: 4526 AN: 112081 Hom.: 86 Cov.: 24

Gnomad AFR AF: 0.0254

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0488

Gnomad ASJ AF: 0.0166

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0979

Gnomad FIN AF: 0.0265

Gnomad MID AF: 0.00833

Gnomad NFE AF: 0.0392

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0403 AC: 4522 AN: 112136 Hom.: 86 Cov.: 24 AF XY: 0.0393 AC XY: 1350 AN XY: 34314

African (AFR) AF: 0.0253 AC: 782 AN: 30939

American (AMR) AF: 0.0486 AC: 516 AN: 10628

Ashkenazi Jewish (ASJ) AF: 0.0166 AC: 44 AN: 2652

East Asian (EAS) AF: 0.169 AC: 596 AN: 3528

South Asian (SAS) AF: 0.0981 AC: 264 AN: 2690

European-Finnish (FIN) AF: 0.0265 AC: 161 AN: 6083

Middle Eastern (MID) AF: 0.00913 AC: 2 AN: 219

European-Non Finnish (NFE) AF: 0.0392 AC: 2086 AN: 53179

Other (OTH) AF: 0.0463 AC: 71 AN: 1533

Alfa AF: 0.0396 Hom.: 317

Bravo AF: 0.0442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.69
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs17267847; hg19: chrX-128777034;