rs7891662

Variant names:

• chrX-71189108-G-A
• rs7891662
• ENST00000450860.1:n.268-5091C>T

Your query was ambiguous. Multiple possible variants found:

• chrX-71189108-G-A
• chrX-71189108-G-C
• chrX-71189108-G-T

Variant summary

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

The ENST00000450860.1(ENSG00000228427):​n.268-5091C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 110,730 control chromosomes in the GnomAD database, including 9,675 homozygotes. There are 15,973 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 0.48 (9675 hom., 15973 hem., cov: 23)
• Consequence: ENSG00000228427 ENST00000450860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 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.268-5091C>T		intron	N/A
	ENSG00000228427	ENST00000652147.3		n.358-5095C>T		intron	N/A
	ENSG00000228427	ENST00000664514.4		n.600-5091C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.484 AC: 53545 AN: 110680 Hom.: 9669 Cov.: 23

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.484 AC: 53587 AN: 110730 Hom.: 9675 Cov.: 23 AF XY: 0.484 AC XY: 15973 AN XY: 32992

African (AFR) AF: 0.617 AC: 18843 AN: 30560

American (AMR) AF: 0.563 AC: 5838 AN: 10368

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 1558 AN: 2632

East Asian (EAS) AF: 0.713 AC: 2490 AN: 3490

South Asian (SAS) AF: 0.561 AC: 1478 AN: 2634

European-Finnish (FIN) AF: 0.364 AC: 2140 AN: 5884

Middle Eastern (MID) AF: 0.596 AC: 127 AN: 213

European-Non Finnish (NFE) AF: 0.379 AC: 19980 AN: 52780

Other (OTH) AF: 0.533 AC: 801 AN: 1503

Alfa AF: 0.424 Hom.: 4861

Bravo AF: 0.506

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.53
PhyloP100		-0.94

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: rs7891662;

hg19: chrX-70408958;