rs6647780

chrX-75604011-G-AchrX-75604011-G-CchrX-75604011-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007068273.1(LOC107985664):n.529-907G>A variant causes a intron, non coding transcript 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: LOC107985664 XR_007068273.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.643

Genes affected

LOC107985664 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107985664	XR_007068273.1	n.529-907G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.182 AC: 20142 AN: 110905 Hom.: 1968 Cov.: 22 AF XY: 0.187 AC XY: 6205 AN XY: 33159

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

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.170

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.179

Alfa AF: 0.174 Hom.: 9265

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6647780; hg19: chrX-74823846;