rs6624543

Variant names:

• chrX-71194792-C-G
• rs6624543
• ENST00000450860.1:n.267+3117G>C

Your query was ambiguous. Multiple possible variants found:

• chrX-71194792-C-G
• chrX-71194792-C-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+3117G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 108,600 control chromosomes in the GnomAD database, including 8,602 homozygotes. There are 13,074 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 0.44 (8602 hom., 13074 hem., cov: 21)
• Consequence: ENSG00000228427 ENST00000450860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273
• Publications: 1 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.628 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+3117G>C		intron	N/A
	ENSG00000228427	ENST00000652147.3		n.357+3117G>C		intron	N/A
	ENSG00000228427	ENST00000664514.4		n.599+3117G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.442 AC: 47938 AN: 108548 Hom.: 8593 Cov.: 21

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.565

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.442 AC: 47980 AN: 108600 Hom.: 8602 Cov.: 21 AF XY: 0.422 AC XY: 13074 AN XY: 30996

African (AFR) AF: 0.636 AC: 18870 AN: 29689

American (AMR) AF: 0.333 AC: 3367 AN: 10112

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1501 AN: 2619

East Asian (EAS) AF: 0.506 AC: 1737 AN: 3434

South Asian (SAS) AF: 0.451 AC: 1152 AN: 2552

European-Finnish (FIN) AF: 0.302 AC: 1663 AN: 5498

Middle Eastern (MID) AF: 0.578 AC: 122 AN: 211

European-Non Finnish (NFE) AF: 0.354 AC: 18541 AN: 52348

Other (OTH) AF: 0.477 AC: 706 AN: 1481

Alfa AF: 0.409 Hom.: 2820

Bravo AF: 0.455

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.87
PhyloP100		0.27

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: rs6624543;

hg19: chrX-70414642;