rs10521631

Variant names:

• chrX-13414963-T-C
• rs10521631
• ENST00000726024.1:n.441+367A>G

Variant summary

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

The ENST00000726024.1(ENSG00000294791):​n.441+367A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 111,534 control chromosomes in the GnomAD database, including 3,986 homozygotes. There are 9,432 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 0.30 (3986 hom., 9432 hem., cov: 24)
• Consequence: ENSG00000294791 ENST00000726024.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.423
• Publications: 0 publications found

Genes affected

ENSG00000294791 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905248	XR_007068395.1	n.537+4606A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294791	ENST00000726024.1	n.441+367A>G		intron_variant	Intron 3 of 3
ENSG00000294791	ENST00000726025.1	n.253+8336A>G		intron_variant	Intron 2 of 2
ENSG00000294791	ENST00000726026.1	n.341+8336A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.297 AC: 33068 AN: 111480 Hom.: 3984 Cov.: 24

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.000837

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.422

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.297 AC: 33073 AN: 111534 Hom.: 3986 Cov.: 24 AF XY: 0.279 AC XY: 9432 AN XY: 33760

African (AFR) AF: 0.245 AC: 7543 AN: 30770

American (AMR) AF: 0.219 AC: 2304 AN: 10542

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 928 AN: 2644

East Asian (EAS) AF: 0.000840 AC: 3 AN: 3573

South Asian (SAS) AF: 0.108 AC: 292 AN: 2714

European-Finnish (FIN) AF: 0.323 AC: 1928 AN: 5974

Middle Eastern (MID) AF: 0.431 AC: 93 AN: 216

European-Non Finnish (NFE) AF: 0.361 AC: 19112 AN: 52909

Other (OTH) AF: 0.288 AC: 438 AN: 1521

Alfa AF: 0.332 Hom.: 2397

Bravo AF: 0.290

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.4
DANN	Benign	0.62
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs10521631; hg19: chrX-13433082;