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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985664	XR_001755885.2	n.529-907G>A		intron_variant	Intron 1 of 3
LOC107985664	XR_001755889.2	n.647-907G>A		intron_variant	Intron 2 of 4
LOC107985664	XR_001755890.2	n.529-907G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302260	ENST00000785233.1	n.419-907G>A		intron_variant	Intron 1 of 5
ENSG00000302260	ENST00000785234.1	n.125-907G>A		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs6647780; hg19: chrX-74823846;