rs5964480

chrX-65995295-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650998.1(ENSG00000237311):n.155-5127G>T variant causes a intron, non coding transcript 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: ENST00000650998.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650998.1	n.155-5127G>T		intron_variant, non_coding_transcript_variant
	ENST00000664185.1	n.103-5127G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.282 AC: 31155 AN: 110664 Hom.: 6618 Cov.: 22 AF XY: 0.257 AC XY: 8464 AN XY: 32912

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

Gnomad4 AFR AF: 0.745

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.0992

Gnomad4 EAS AF: 0.000284

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.0678

Gnomad4 NFE AF: 0.0995

Gnomad4 OTH AF: 0.230

Alfa AF: 0.175 Hom.: 3868

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.64
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5964480; hg19: chrX-65215137;