rs2038265

Variant names:

• chrX-142036216-T-C
• rs2038265
• ENST00000664519.1:n.222+101499T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664519.1(ENSG00000288098):​n.222+101499T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 111,718 control chromosomes in the GnomAD database, including 1,206 homozygotes. There are 5,198 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 0.17 (1206 hom., 5198 hem., cov: 23)
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.50

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.178 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
ENSG00000288098	ENST00000664519.1	n.222+101499T>C		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.167 AC: 18611 AN: 111665 Hom.: 1206 Cov.: 23 AF XY: 0.153 AC XY: 5194 AN XY: 33857

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.0819

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.0952

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.167 AC: 18611 AN: 111718 Hom.: 1206 Cov.: 23 AF XY: 0.153 AC XY: 5198 AN XY: 33920

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.0940

Gnomad4 SAS AF: 0.0951

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.185

Alfa AF: 0.176 Hom.: 12115

Bravo AF: 0.172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.017
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2038265; hg19: chrX-141124002;