rs5981378

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785233.1. 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
	ENSG00000302260	ENST00000785233.1		n.523+3114C>T		intron	N/A
	ENSG00000302260	ENST00000785234.1		n.229+3114C>T		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs5981378;

hg19: chrX-74827971;