X-113118620-T-C

Variant names:

• chrX-113118620-T-C
• rs12164331
• ENST00000651919.1:n.346+45502T>C

Variant summary

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

The ENST00000651919.1(ENSG00000286072):​n.346+45502T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 111,008 control chromosomes in the GnomAD database, including 5,336 homozygotes. There are 11,418 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 0.35 (5336 hom., 11418 hem., cov: 23)
• Consequence: ENSG00000286072 ENST00000651919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 1 publications found

Genes affected

ENSG00000286072 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928437	NR_110399.2	n.231+6555T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286072	ENST00000651919.1	n.346+45502T>C		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.352 AC: 39034 AN: 110958 Hom.: 5340 Cov.: 23

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.375

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.352 AC: 39045 AN: 111008 Hom.: 5336 Cov.: 23 AF XY: 0.343 AC XY: 11418 AN XY: 33252

African (AFR) AF: 0.214 AC: 6576 AN: 30722

American (AMR) AF: 0.314 AC: 3291 AN: 10466

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 896 AN: 2635

East Asian (EAS) AF: 0.495 AC: 1715 AN: 3464

South Asian (SAS) AF: 0.367 AC: 974 AN: 2654

European-Finnish (FIN) AF: 0.446 AC: 2624 AN: 5878

Middle Eastern (MID) AF: 0.354 AC: 75 AN: 212

European-Non Finnish (NFE) AF: 0.419 AC: 22124 AN: 52800

Other (OTH) AF: 0.342 AC: 516 AN: 1509

Alfa AF: 0.371 Hom.: 2444

Bravo AF: 0.339

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.71
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs12164331; hg19: chrX-112361848;