rs6623918

chrX-87161008-G-AchrX-87161008-G-CchrX-87161008-G-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 0.068 in 111,096 control chromosomes in the GnomAD database, including 259 homozygotes. There are 2,326 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 0.068 (259 hom., 2326 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.247 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: 0.0681 AC: 7560 AN: 111043 Hom.: 259 Cov.: 22 AF XY: 0.0699 AC XY: 2326 AN XY: 33293

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0470

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.0284

Gnomad MID AF: 0.0417

Gnomad NFE AF: 0.0373

Gnomad OTH AF: 0.0628

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

GnomAD4 genome AF: 0.0680 AC: 7558 AN: 111096 Hom.: 259 Cov.: 22 AF XY: 0.0697 AC XY: 2326 AN XY: 33356

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0329

Gnomad4 ASJ AF: 0.0470

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.0284

Gnomad4 NFE AF: 0.0373

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.0464 Hom.: 256

Bravo AF: 0.0671

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.53
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6623918; hg19: chrX-86416011;