rs6647780

Variant names:

• chrX-75604011-G-A
• rs6647780
• ENST00000785233.1:n.419-907G>A

Your query was ambiguous. Multiple possible variants found:

• chrX-75604011-G-A
• chrX-75604011-G-C
• chrX-75604011-G-T

Variant summary

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

The ENST00000785233.1(ENSG00000302260):​n.419-907G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 110,955 control chromosomes in the GnomAD database, including 1,972 homozygotes. There are 6,205 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 0.18 (1972 hom., 6205 hem., cov: 22)
• Consequence: ENSG00000302260 ENST00000785233.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.643
• Publications: 2 publications found

Genes affected

ENSG00000302260 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785233.1. 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
	ENSG00000302260	ENST00000785233.1		n.419-907G>A		intron	N/A
	ENSG00000302260	ENST00000785234.1		n.125-907G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.182 AC: 20142 AN: 110905 Hom.: 1968 Cov.: 22

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.0980

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.182 AC: 20151 AN: 110955 Hom.: 1972 Cov.: 22 AF XY: 0.187 AC XY: 6205 AN XY: 33219

African (AFR) AF: 0.116 AC: 3534 AN: 30552

American (AMR) AF: 0.286 AC: 2988 AN: 10443

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 311 AN: 2630

East Asian (EAS) AF: 0.854 AC: 2950 AN: 3453

South Asian (SAS) AF: 0.360 AC: 927 AN: 2576

European-Finnish (FIN) AF: 0.170 AC: 1011 AN: 5948

Middle Eastern (MID) AF: 0.116 AC: 25 AN: 215

European-Non Finnish (NFE) AF: 0.152 AC: 8067 AN: 52943

Other (OTH) AF: 0.179 AC: 271 AN: 1511

Alfa AF: 0.173 Hom.: 12092

Bravo AF: 0.197

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.8
DANN	Benign	0.78
PhyloP100		0.64

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: rs6647780;

hg19: chrX-74823846;