rs6525037

Variant names:

• chrX-65955617-G-T
• rs6525037
• ENST00000650998.1:n.154+23044G>T

Variant summary

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

The ENST00000650998.1(ENSG00000237311):​n.154+23044G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.25 (4094 hom., 4122 hem., cov: 19)
• Consequence: ENSG00000237311 ENST00000650998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.596
• Publications: 1 publications found

Genes affected

ENSG00000237311 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.603 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
ENSG00000237311	ENST00000650998.1	n.154+23044G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.248 AC: 22354 AN: 89985 Hom.: 4095 Cov.: 19

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.0989

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.0691

Gnomad FIN AF: 0.0532

Gnomad MID AF: 0.135

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.248 AC: 22358 AN: 89985 Hom.: 4094 Cov.: 19 AF XY: 0.192 AC XY: 4122 AN XY: 21515

African (AFR) AF: 0.611 AC: 15092 AN: 24705

American (AMR) AF: 0.171 AC: 1416 AN: 8264

Ashkenazi Jewish (ASJ) AF: 0.0989 AC: 216 AN: 2185

East Asian (EAS) AF: 0.0169 AC: 50 AN: 2950

South Asian (SAS) AF: 0.0702 AC: 146 AN: 2079

European-Finnish (FIN) AF: 0.0532 AC: 197 AN: 3703

Middle Eastern (MID) AF: 0.147 AC: 22 AN: 150

European-Non Finnish (NFE) AF: 0.110 AC: 4862 AN: 44229

Other (OTH) AF: 0.196 AC: 231 AN: 1181

Alfa AF: 0.212 Hom.: 4506

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.6
DANN	Benign	0.22
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs6525037; hg19: chrX-65175459; COSMIC: COSV71695621;