rs6624541

Variant names:

• chrX-71193094-G-A
• rs6624541
• ENST00000450860.1:n.267+4815C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000228427 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000450860.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228427	ENST00000450860.1	TSL:3	n.267+4815C>T		intron	N/A
	ENSG00000228427	ENST00000652147.3		n.357+4815C>T		intron	N/A
	ENSG00000228427	ENST00000664514.4		n.599+4815C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.490 AC: 53326 AN: 108856 Hom.: 10072 Cov.: 21

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

African (AFR) AF: 0.640 AC: 19181 AN: 29955

American (AMR) AF: 0.568 AC: 5721 AN: 10073

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 1552 AN: 2618

East Asian (EAS) AF: 0.709 AC: 2417 AN: 3410

South Asian (SAS) AF: 0.557 AC: 1389 AN: 2494

European-Finnish (FIN) AF: 0.362 AC: 2023 AN: 5583

Middle Eastern (MID) AF: 0.608 AC: 132 AN: 217

European-Non Finnish (NFE) AF: 0.378 AC: 19826 AN: 52399

Other (OTH) AF: 0.536 AC: 802 AN: 1496

Alfa AF: 0.220 Hom.: 930

Bravo AF: 0.514

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.44
PhyloP100		-0.96

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6624541;

hg19: chrX-70412944;