chrX-75608136-C-T

Variant names:

• chrX-75608136-C-T
• rs5981378
• ENST00000785233.1:n.523+3114C>T

Variant summary

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

The ENST00000785233.1(ENSG00000302260):​n.523+3114C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0751 in 111,876 control chromosomes in the GnomAD database, including 459 homozygotes. There are 2,295 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 0.075 (459 hom., 2295 hem., cov: 22)
• Consequence: ENSG00000302260 ENST00000785233.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 0 publications found

Genes affected

ENSG00000302260 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985664	XR_001755885.2	n.633+3114C>T		intron_variant	Intron 2 of 3
LOC107985664	XR_001755889.2	n.751+3114C>T		intron_variant	Intron 3 of 4
LOC107985664	XR_001755890.2	n.633+3114C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302260	ENST00000785233.1	n.523+3114C>T		intron_variant	Intron 2 of 5
ENSG00000302260	ENST00000785234.1	n.229+3114C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0748 AC: 8368 AN: 111824 Hom.: 456 Cov.: 22

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0324

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.0242

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0148

Gnomad MID AF: 0.0168

Gnomad NFE AF: 0.0272

Gnomad OTH AF: 0.0576

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

GnomAD4 genome AF: 0.0751 AC: 8405 AN: 111876 Hom.: 459 Cov.: 22 AF XY: 0.0673 AC XY: 2295 AN XY: 34088

African (AFR) AF: 0.193 AC: 5919 AN: 30658

American (AMR) AF: 0.0326 AC: 345 AN: 10599

Ashkenazi Jewish (ASJ) AF: 0.0291 AC: 77 AN: 2645

East Asian (EAS) AF: 0.0243 AC: 86 AN: 3542

South Asian (SAS) AF: 0.131 AC: 349 AN: 2665

European-Finnish (FIN) AF: 0.0148 AC: 91 AN: 6162

Middle Eastern (MID) AF: 0.0185 AC: 4 AN: 216

European-Non Finnish (NFE) AF: 0.0272 AC: 1445 AN: 53176

Other (OTH) AF: 0.0582 AC: 89 AN: 1530

Alfa AF: 0.0451 Hom.: 3785

Bravo AF: 0.0814

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.28
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs5981378; hg19: chrX-74827971;