rs7885458

chrX-6302433-T-C

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 0.303 in 111,402 control chromosomes in the GnomAD database, including 4,210 homozygotes. There are 9,619 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 0.30 (4210 hom., 9619 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.303 AC: 33748 AN: 111349 Hom.: 4208 Cov.: 23 AF XY: 0.285 AC XY: 9579 AN XY: 33593

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.0858

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.303 AC: 33788 AN: 111402 Hom.: 4210 Cov.: 23 AF XY: 0.286 AC XY: 9619 AN XY: 33656

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.252

Gnomad4 EAS AF: 0.0852

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.209

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.290

Alfa AF: 0.258 Hom.: 23712

Bravo AF: 0.318

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.0070
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7885458; hg19: chrX-6220474;