rs5969041

Positions:

• chrX-86988257-A-G
• chrX-86988257-A-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 0.412 in 110,161 control chromosomes in the GnomAD database, including 7,092 homozygotes. There are 12,990 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 0.41 (7092 hom., 12990 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 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: 0.412 AC: 45358 AN: 110112 Hom.: 7089 Cov.: 22 AF XY: 0.400 AC XY: 12951 AN XY: 32376

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.409

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.412 AC: 45394 AN: 110161 Hom.: 7092 Cov.: 22 AF XY: 0.400 AC XY: 12990 AN XY: 32435

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.513

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.417

Alfa AF: 0.268 Hom.: 2020

Bravo AF: 0.434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.6
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5969041; hg19: chrX-86243260;