chrX-42110232-C-T

Variant names:

• chrX-42110232-C-T
• rs5918294
• ENST00000723425.1:n.65-162C>T

Variant summary

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

The ENST00000723425.1(ENSG00000294407):​n.65-162C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 110,580 control chromosomes in the GnomAD database, including 4,222 homozygotes. There are 9,908 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 0.31 (4222 hom., 9908 hem., cov: 23)
• Consequence: ENSG00000294407 ENST00000723425.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572
• Publications: 1 publications found

Genes affected

ENSG00000294407 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000723425.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294407	ENST00000723425.1		n.65-162C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.311 AC: 34322 AN: 110530 Hom.: 4221 Cov.: 23

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.368

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.310 AC: 34334 AN: 110580 Hom.: 4222 Cov.: 23 AF XY: 0.302 AC XY: 9908 AN XY: 32854

African (AFR) AF: 0.181 AC: 5513 AN: 30504

American (AMR) AF: 0.367 AC: 3826 AN: 10411

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1090 AN: 2634

East Asian (EAS) AF: 0.154 AC: 537 AN: 3490

South Asian (SAS) AF: 0.244 AC: 629 AN: 2583

European-Finnish (FIN) AF: 0.337 AC: 1951 AN: 5792

Middle Eastern (MID) AF: 0.344 AC: 74 AN: 215

European-Non Finnish (NFE) AF: 0.380 AC: 20058 AN: 52784

Other (OTH) AF: 0.314 AC: 469 AN: 1496

Alfa AF: 0.351 Hom.: 41666

Bravo AF: 0.303

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.084
DANN	Benign	0.57
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs5918294; hg19: chrX-41969485;