chrX-123496525-T-C

Variant names:

• chrX-123496525-T-C
• rs4474149
• ENST00000825206.1:n.62+17832A>G

Variant summary

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

The ENST00000825206.1(ENSG00000307341):​n.62+17832A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 110,762 control chromosomes in the GnomAD database, including 5,174 homozygotes. There are 11,439 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 0.36 (5174 hom., 11439 hem., cov: 22)
• Consequence: ENSG00000307341 ENST00000825206.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.583
• Publications: 2 publications found

Genes affected

ENSG00000307341 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 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
ENSG00000307341	ENST00000825206.1	n.62+17832A>G		intron_variant	Intron 1 of 6
ENSG00000307341	ENST00000825207.1	n.174+17832A>G		intron_variant	Intron 1 of 4
ENSG00000307341	ENST00000825208.1	n.155+17832A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.356 AC: 39378 AN: 110709 Hom.: 5170 Cov.: 22

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.356 AC: 39403 AN: 110762 Hom.: 5174 Cov.: 22 AF XY: 0.346 AC XY: 11439 AN XY: 33028

African (AFR) AF: 0.304 AC: 9274 AN: 30494

American (AMR) AF: 0.382 AC: 3986 AN: 10428

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 957 AN: 2630

East Asian (EAS) AF: 0.559 AC: 1944 AN: 3480

South Asian (SAS) AF: 0.273 AC: 721 AN: 2645

European-Finnish (FIN) AF: 0.344 AC: 2012 AN: 5844

Middle Eastern (MID) AF: 0.355 AC: 75 AN: 211

European-Non Finnish (NFE) AF: 0.372 AC: 19650 AN: 52845

Other (OTH) AF: 0.363 AC: 549 AN: 1511

Alfa AF: 0.352 Hom.: 3927

Bravo AF: 0.364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.5
DANN	Benign	0.92
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs4474149; hg19: chrX-122630376;