rs1656651

Positions:

• chrX-10948474-G-A

Variant summary

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

The NR_186561.1(HCCS-DT):​n.501-88128C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 110,967 control chromosomes in the GnomAD database, including 3,073 homozygotes. There are 7,299 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 0.23 (3073 hom., 7299 hem., cov: 23)
• Consequence: HCCS-DT NR_186561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.574

Genes affected

HCCS-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HCCS-DT	NR_186561.1	n.501-88128C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HCCS-DT	ENST00000608176.5	n.318-88128C>T		intron_variant		5
HCCS-DT	ENST00000658066.1	n.516+15408C>T		intron_variant
HCCS-DT	ENST00000669054.1	n.583-88128C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.234 AC: 25918 AN: 110912 Hom.: 3074 Cov.: 23 AF XY: 0.220 AC XY: 7301 AN XY: 33174

Gnomad AFR AF: 0.0486

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.000845

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.292

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.233 AC: 25899 AN: 110967 Hom.: 3073 Cov.: 23 AF XY: 0.220 AC XY: 7299 AN XY: 33239

Gnomad4 AFR AF: 0.0485

Gnomad4 AMR AF: 0.170

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.000847

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.231

Alfa AF: 0.311 Hom.: 3904

Bravo AF: 0.219

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1656651; hg19: chrX-10966594;