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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985688	XR_001755878.2	n.286-6476C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228427	ENST00000450860.1	n.268-6476C>T		intron_variant	Intron 1 of 1	3
ENSG00000228427	ENST00000652147.3	n.358-6480C>T		intron_variant	Intron 1 of 1
ENSG00000228427	ENST00000664514.4	n.600-6476C>T		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs7057179; hg19: chrX-70410343;