rs5964480

Variant names:

• chrX-65995295-G-T
• rs5964480
• ENST00000650998.1:n.155-5127G>T

Variant summary

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

The ENST00000650998.1(ENSG00000237311):​n.155-5127G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 110,719 control chromosomes in the GnomAD database, including 6,622 homozygotes. There are 8,518 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 0.28 (6622 hom., 8518 hem., cov: 22)
• Consequence: ENSG00000237311 ENST00000650998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 1 publications found

Genes affected

ENSG00000237311 (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 (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650998.1. 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
	ENSG00000237311	ENST00000650998.1		n.155-5127G>T		intron	N/A
	ENSG00000237311	ENST00000664185.1		n.103-5127G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.282 AC: 31155 AN: 110664 Hom.: 6618 Cov.: 22

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.000283

Gnomad SAS AF: 0.0725

Gnomad FIN AF: 0.0678

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.282 AC: 31219 AN: 110719 Hom.: 6622 Cov.: 22 AF XY: 0.258 AC XY: 8518 AN XY: 32977

African (AFR) AF: 0.745 AC: 22501 AN: 30183

American (AMR) AF: 0.197 AC: 2050 AN: 10432

Ashkenazi Jewish (ASJ) AF: 0.0992 AC: 262 AN: 2641

East Asian (EAS) AF: 0.000284 AC: 1 AN: 3519

South Asian (SAS) AF: 0.0742 AC: 196 AN: 2641

European-Finnish (FIN) AF: 0.0678 AC: 406 AN: 5992

Middle Eastern (MID) AF: 0.146 AC: 31 AN: 212

European-Non Finnish (NFE) AF: 0.0995 AC: 5267 AN: 52925

Other (OTH) AF: 0.230 AC: 345 AN: 1499

Alfa AF: 0.200 Hom.: 6910

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.64
DANN	Benign	0.42
PhyloP100		-0.032

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: rs5964480;

hg19: chrX-65215137;