X-128921593-G-T

Position:

• chrX-128921593-G-T

Variant summary

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

The ENST00000660383.1(ENSG00000225689):​n.567+110757C>A 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 0.36 in 111,248 control chromosomes in the GnomAD database, including 5,737 homozygotes. There are 11,848 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 0.36 (5737 hom., 11848 hem., cov: 24)
• Consequence: ENST00000660383.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124905213	XR_007068324.1	n.1643-6520C>A		intron_variant, non_coding_transcript_variant
LOC124905213	XR_007068316.1	n.5762-6520C>A		intron_variant, non_coding_transcript_variant
LOC124905213	XR_007068325.1	n.7171-6520C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000660383.1	n.567+110757C>A		intron_variant, non_coding_transcript_variant
	ENST00000653849.1	n.1436-86917C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.360 AC: 39978 AN: 111194 Hom.: 5730 Cov.: 24 AF XY: 0.353 AC XY: 11806 AN XY: 33430

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.360 AC: 40030 AN: 111248 Hom.: 5737 Cov.: 24 AF XY: 0.354 AC XY: 11848 AN XY: 33494

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.300

Gnomad4 OTH AF: 0.329

Alfa AF: 0.333 Hom.: 2198

Bravo AF: 0.360

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4830105; hg19: chrX-128055571;