rs9697841

Variant names:

• chrX-50904937-T-G
• rs9697841

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 0.181 in 110,013 control chromosomes in the GnomAD database, including 2,848 homozygotes. There are 5,176 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 0.18 (2848 hom., 5176 hem., cov: 21)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.180 AC: 19812 AN: 109964 Hom.: 2845 Cov.: 21 AF XY: 0.159 AC XY: 5146 AN XY: 32282

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.0262

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.0849

Gnomad EAS AF: 0.0495

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0496

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.181 AC: 19858 AN: 110013 Hom.: 2848 Cov.: 21 AF XY: 0.160 AC XY: 5176 AN XY: 32341

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.0765

Gnomad4 ASJ AF: 0.0849

Gnomad4 EAS AF: 0.0491

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.0496

Gnomad4 NFE AF: 0.0641

Gnomad4 OTH AF: 0.155

Alfa AF: 0.132 Hom.: 811

Bravo AF: 0.198

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.1
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9697841; hg19: chrX-50647937;