rs2038265

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.182 AC: 5602 AN: 30761

American (AMR) AF: 0.139 AC: 1460 AN: 10526

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 671 AN: 2633

East Asian (EAS) AF: 0.0940 AC: 333 AN: 3544

South Asian (SAS) AF: 0.0951 AC: 256 AN: 2692

European-Finnish (FIN) AF: 0.115 AC: 700 AN: 6074

Middle Eastern (MID) AF: 0.269 AC: 58 AN: 216

European-Non Finnish (NFE) AF: 0.173 AC: 9193 AN: 53065

Other (OTH) AF: 0.185 AC: 282 AN: 1523

Alfa AF: 0.176 Hom.: 16272

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
PhyloP100		-4.5

Splicing

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

Other links and lift over

dbSNP: rs2038265; hg19: chrX-141124002;