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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726024.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294791	ENST00000726024.1		n.441+367A>G		intron	N/A
	ENSG00000294791	ENST00000726025.1		n.253+8336A>G		intron	N/A
	ENSG00000294791	ENST00000726026.1		n.341+8336A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10521631;

hg19: chrX-13433082;