rs7056485

Variant names:

• chrX-142079179-C-T
• rs7056485
• ENST00000664519.1:n.223-116528C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000664519.1(ENSG00000288098):​n.223-116528C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.56 (13449 hom., 17436 hem., cov: 21)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000288098 ENST00000664519.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 2 publications found

Genes affected

ENSG00000288098 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288098	ENST00000664519.1	n.223-116528C>T		intron_variant	Intron 1 of 9

Frequencies

GnomAD3 genomes AF: 0.560 AC: 60916 AN: 108866 Hom.: 13448 Cov.: 21

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.601

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.560 AC: 60968 AN: 108916 Hom.: 13449 Cov.: 21 AF XY: 0.557 AC XY: 17436 AN XY: 31280

African (AFR) AF: 0.788 AC: 23484 AN: 29813

American (AMR) AF: 0.684 AC: 6922 AN: 10119

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1388 AN: 2615

East Asian (EAS) AF: 0.651 AC: 2202 AN: 3385

South Asian (SAS) AF: 0.520 AC: 1292 AN: 2483

European-Finnish (FIN) AF: 0.467 AC: 2602 AN: 5577

Middle Eastern (MID) AF: 0.502 AC: 104 AN: 207

European-Non Finnish (NFE) AF: 0.417 AC: 21943 AN: 52577

Other (OTH) AF: 0.602 AC: 885 AN: 1469

Alfa AF: 0.493 Hom.: 55898

Bravo AF: 0.596

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.42
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs7056485; hg19: chrX-141166965;