rs7057179

Variant names:

• chrX-71190493-G-A
• rs7057179
• ENST00000450860.1:n.268-6476C>T

Variant summary

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

The ENST00000450860.1(ENSG00000228427):​n.268-6476C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 110,556 control chromosomes in the GnomAD database, including 7,106 homozygotes. There are 13,421 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 0.41 (7106 hom., 13421 hem., cov: 23)
• Consequence: ENSG00000228427 ENST00000450860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.325
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 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.268-6476C>T		intron	N/A
	ENSG00000228427	ENST00000652147.3		n.358-6480C>T		intron	N/A
	ENSG00000228427	ENST00000664514.4		n.600-6476C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.413 AC: 45650 AN: 110504 Hom.: 7099 Cov.: 23

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.572

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.413 AC: 45691 AN: 110556 Hom.: 7106 Cov.: 23 AF XY: 0.408 AC XY: 13421 AN XY: 32874

African (AFR) AF: 0.489 AC: 14848 AN: 30349

American (AMR) AF: 0.518 AC: 5353 AN: 10332

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1455 AN: 2640

East Asian (EAS) AF: 0.625 AC: 2172 AN: 3473

South Asian (SAS) AF: 0.493 AC: 1297 AN: 2632

European-Finnish (FIN) AF: 0.328 AC: 1934 AN: 5902

Middle Eastern (MID) AF: 0.586 AC: 126 AN: 215

European-Non Finnish (NFE) AF: 0.331 AC: 17471 AN: 52854

Other (OTH) AF: 0.484 AC: 726 AN: 1499

Alfa AF: 0.380 Hom.: 2529

Bravo AF: 0.436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.66
PhyloP100		0.33

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: rs7057179;

hg19: chrX-70410343;