rs707254

Variant names:

• chrX-131612836-A-G
• rs707254
• ENST00000836463.1:n.764+1645A>G

Your query was ambiguous. Multiple possible variants found:

• chrX-131612836-A-G
• chrX-131612836-A-T

Variant summary

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

The ENST00000836463.1(ENSG00000286060):​n.764+1645A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 110,365 control chromosomes in the GnomAD database, including 4,584 homozygotes. There are 10,514 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 0.32 (4584 hom., 10514 hem., cov: 22)
• Consequence: ENSG00000286060 ENST00000836463.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 1 publications found

Genes affected

ENSG00000286060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

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
ENSG00000286060	ENST00000836463.1	n.764+1645A>G		intron_variant	Intron 5 of 6
ENSG00000286060	ENST00000836464.1	n.438-4547A>G		intron_variant	Intron 4 of 5
ENSG00000286060	ENST00000836465.1	n.629+1645A>G		intron_variant	Intron 5 of 6

Frequencies

GnomAD3 genomes AF: 0.324 AC: 35789 AN: 110311 Hom.: 4582 Cov.: 22

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.324 AC: 35796 AN: 110365 Hom.: 4584 Cov.: 22 AF XY: 0.322 AC XY: 10514 AN XY: 32635

African (AFR) AF: 0.172 AC: 5237 AN: 30518

American (AMR) AF: 0.429 AC: 4410 AN: 10287

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 924 AN: 2627

East Asian (EAS) AF: 0.501 AC: 1733 AN: 3458

South Asian (SAS) AF: 0.288 AC: 741 AN: 2574

European-Finnish (FIN) AF: 0.388 AC: 2255 AN: 5805

Middle Eastern (MID) AF: 0.225 AC: 48 AN: 213

European-Non Finnish (NFE) AF: 0.374 AC: 19726 AN: 52711

Other (OTH) AF: 0.344 AC: 516 AN: 1498

Alfa AF: 0.348 Hom.: 13946

Bravo AF: 0.326

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs707254; hg19: chrX-130746838;