rs760109

Variant names:

• chrX-151384050-A-G
• rs760109
• ENST00000664896.1:n.319+11827T>C

Variant summary

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

The ENST00000664896.1(ENSG00000287918):​n.319+11827T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 111,276 control chromosomes in the GnomAD database, including 5,853 homozygotes. There are 11,158 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 0.34 (5853 hom., 11158 hem., cov: 23)
• Consequence: ENSG00000287918 ENST00000664896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307
• Publications: 2 publications found

Genes affected

ENSG00000287918 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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
ENSG00000287918	ENST00000664896.1	n.319+11827T>C		intron_variant	Intron 1 of 3
ENSG00000287918	ENST00000664935.1	n.588+12381T>C		intron_variant	Intron 1 of 1
ENSG00000287918	ENST00000668689.1	n.1266+11827T>C		intron_variant	Intron 1 of 1
ENSG00000287918	ENST00000811648.1	n.619+12395T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.339 AC: 37711 AN: 111222 Hom.: 5847 Cov.: 23

Gnomad AFR AF: 0.0854

Gnomad AMI AF: 0.551

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.339 AC: 37720 AN: 111276 Hom.: 5853 Cov.: 23 AF XY: 0.333 AC XY: 11158 AN XY: 33498

African (AFR) AF: 0.0852 AC: 2624 AN: 30808

American (AMR) AF: 0.283 AC: 2990 AN: 10577

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1122 AN: 2632

East Asian (EAS) AF: 0.135 AC: 476 AN: 3530

South Asian (SAS) AF: 0.276 AC: 729 AN: 2642

European-Finnish (FIN) AF: 0.516 AC: 3009 AN: 5830

Middle Eastern (MID) AF: 0.379 AC: 81 AN: 214

European-Non Finnish (NFE) AF: 0.488 AC: 25804 AN: 52846

Other (OTH) AF: 0.337 AC: 512 AN: 1520

Alfa AF: 0.421 Hom.: 37460

Bravo AF: 0.310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.50
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs760109; hg19: chrX-150552522;