X-71193185-T-C

Variant names:

• chrX-71193185-T-C
• rs6624542
• ENST00000450860.1:n.267+4724A>G

Variant summary

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

The ENST00000450860.1(ENSG00000228427):​n.267+4724A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 110,052 control chromosomes in the GnomAD database, including 10,262 homozygotes. There are 15,807 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 (10262 hom., 15807 hem., cov: 22)
• Consequence: ENSG00000228427 ENST00000450860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• 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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.687 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+4724A>G		intron	N/A
	ENSG00000228427	ENST00000652147.3		n.357+4724A>G		intron	N/A
	ENSG00000228427	ENST00000664514.4		n.599+4724A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.493 AC: 54241 AN: 109998 Hom.: 10254 Cov.: 22

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.493 AC: 54295 AN: 110052 Hom.: 10262 Cov.: 22 AF XY: 0.489 AC XY: 15807 AN XY: 32318

African (AFR) AF: 0.651 AC: 19685 AN: 30261

American (AMR) AF: 0.570 AC: 5798 AN: 10172

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 1561 AN: 2633

East Asian (EAS) AF: 0.710 AC: 2482 AN: 3494

South Asian (SAS) AF: 0.563 AC: 1463 AN: 2600

European-Finnish (FIN) AF: 0.362 AC: 2063 AN: 5706

Middle Eastern (MID) AF: 0.600 AC: 129 AN: 215

European-Non Finnish (NFE) AF: 0.378 AC: 19964 AN: 52804

Other (OTH) AF: 0.543 AC: 813 AN: 1496

Alfa AF: 0.445 Hom.: 3128

Bravo AF: 0.518

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.52
DANN	Benign	0.17
PhyloP100		-1.3

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: rs6624542;

hg19: chrX-70413035;