rs6616002

Positions:

• chrX-98435234-C-A
• chrX-98435234-C-G
• chrX-98435234-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 0.305 in 111,200 control chromosomes in the GnomAD database, including 4,061 homozygotes. There are 10,364 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 0.31 (4061 hom., 10364 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.951

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.305 AC: 33935 AN: 111148 Hom.: 4069 Cov.: 23 AF XY: 0.309 AC XY: 10348 AN XY: 33436

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.305 AC: 33929 AN: 111200 Hom.: 4061 Cov.: 23 AF XY: 0.309 AC XY: 10364 AN XY: 33498

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.303

Gnomad4 OTH AF: 0.346

Alfa AF: 0.301 Hom.: 12552

Bravo AF: 0.322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6616002; hg19: chrX-97690232;