rs2038265

Positions:

• chrX-142036216-T-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, non coding transcript 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: ENST00000664519.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.50

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664519.1	n.222+101499T>C		intron_variant, non_coding_transcript_variant

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;