rs5945608

Variant names:

• chrX-51458235-C-A
• rs5945608
• ENST00000455931.2:n.758-7172C>A

Your query was ambiguous. Multiple possible variants found:

• chrX-51458235-C-A
• chrX-51458235-C-G

Variant summary

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

The ENST00000455931.2(ENSG00000226530):​n.758-7172C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 111,841 control chromosomes in the GnomAD database, including 948 homozygotes. There are 4,519 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 0.13 (948 hom., 4519 hem., cov: 23)
• Consequence: ENSG00000226530 ENST00000455931.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 1 publications found

Genes affected

ENSG00000226530 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455931.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000226530	ENST00000455931.2	TSL:3	n.758-7172C>A		intron	N/A
	ENSG00000226530	ENST00000767703.1		n.851+403C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.134 AC: 15006 AN: 111790 Hom.: 948 Cov.: 23

Gnomad AFR AF: 0.0315

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.0370

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.134 AC: 15012 AN: 111841 Hom.: 948 Cov.: 23 AF XY: 0.133 AC XY: 4519 AN XY: 34077

African (AFR) AF: 0.0315 AC: 973 AN: 30888

American (AMR) AF: 0.114 AC: 1213 AN: 10659

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 266 AN: 2651

East Asian (EAS) AF: 0.0374 AC: 133 AN: 3553

South Asian (SAS) AF: 0.156 AC: 415 AN: 2660

European-Finnish (FIN) AF: 0.222 AC: 1326 AN: 5968

Middle Eastern (MID) AF: 0.108 AC: 23 AN: 213

European-Non Finnish (NFE) AF: 0.194 AC: 10271 AN: 53054

Other (OTH) AF: 0.125 AC: 191 AN: 1524

Alfa AF: 0.137 Hom.: 4423

Bravo AF: 0.122

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.89
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs5945608; hg19: chrX-51201087;