rs6624541

Positions:

• chrX-71193094-G-A
• chrX-71193094-G-C
• chrX-71193094-G-T

Variant summary

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

The ENST00000450860.1(ENSG00000228427):​n.267+4815C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 108,909 control chromosomes in the GnomAD database, including 10,080 homozygotes. There are 15,202 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 0.49 (10080 hom., 15202 hem., cov: 21)
• Consequence: ENSG00000228427 ENST00000450860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.963

Genes affected

ENSG00000228427 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985688	XR_001755878.2	n.285+4815C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000228427	ENST00000450860.1	n.267+4815C>T		intron_variant		3
ENSG00000228427	ENST00000652147.2	n.321+4815C>T		intron_variant
ENSG00000228427	ENST00000664514.3	n.331+4815C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.490 AC: 53326 AN: 108856 Hom.: 10072 Cov.: 21 AF XY: 0.486 AC XY: 15161 AN XY: 31214

Gnomad AFR AF: 0.640

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.490 AC: 53376 AN: 108909 Hom.: 10080 Cov.: 21 AF XY: 0.486 AC XY: 15202 AN XY: 31275

Gnomad4 AFR AF: 0.640

Gnomad4 AMR AF: 0.568

Gnomad4 ASJ AF: 0.593

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.536

Alfa AF: 0.220 Hom.: 930

Bravo AF: 0.514

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6624541; hg19: chrX-70412944;