rs6644385

Positions:

• chrX-861671-C-T

Variant summary

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

The variant allele was found at a frequency of 0.487 in 148,634 control chromosomes in the GnomAD database, including 20,369 homozygotes. There are 35,704 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 (20369 hom., 35704 hem., cov: 29)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.861671C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.486 AC: 72229 AN: 148516 Hom.: 20340 Cov.: 29 AF XY: 0.493 AC XY: 35613 AN XY: 72304

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.397

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.487 AC: 72312 AN: 148634 Hom.: 20369 Cov.: 29 AF XY: 0.493 AC XY: 35704 AN XY: 72432

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.488

Gnomad4 OTH AF: 0.509

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6644385; hg19: chrX-822406;