rs6625761

Variant names:

• chrX-71191723-G-A
• rs6625761
• ENST00000450860.1:n.267+6186C>T

Variant summary

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

The ENST00000450860.1(ENSG00000228427):​n.267+6186C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 110,203 control chromosomes in the GnomAD database, including 9,726 homozygotes. There are 15,797 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 (9726 hom., 15797 hem., cov: 22)
• Consequence: ENSG00000228427 ENST00000450860.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878
• 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 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+6186C>T		intron	N/A
	ENSG00000228427	ENST00000652147.3		n.357+6186C>T		intron	N/A
	ENSG00000228427	ENST00000664514.4		n.599+6186C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 53422 AN: 110151 Hom.: 9719 Cov.: 22

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.597

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.485 AC: 53467 AN: 110203 Hom.: 9726 Cov.: 22 AF XY: 0.486 AC XY: 15797 AN XY: 32509

African (AFR) AF: 0.619 AC: 18741 AN: 30299

American (AMR) AF: 0.566 AC: 5834 AN: 10309

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 1560 AN: 2635

East Asian (EAS) AF: 0.716 AC: 2503 AN: 3496

South Asian (SAS) AF: 0.562 AC: 1473 AN: 2620

European-Finnish (FIN) AF: 0.363 AC: 2094 AN: 5776

Middle Eastern (MID) AF: 0.608 AC: 129 AN: 212

European-Non Finnish (NFE) AF: 0.379 AC: 19988 AN: 52681

Other (OTH) AF: 0.537 AC: 809 AN: 1507

Alfa AF: 0.440 Hom.: 3077

Bravo AF: 0.507

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.36
DANN	Benign	0.43
PhyloP100		-0.88

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: rs6625761;

hg19: chrX-70411573;