rs5971535

Variant names:

• chrX-30994973-G-A
• rs5971535

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 0.114 in 111,600 control chromosomes in the GnomAD database, including 649 homozygotes. There are 3,530 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 0.11 (649 hom., 3530 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.186 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: 0.114 AC: 12720 AN: 111544 Hom.: 648 Cov.: 22 AF XY: 0.104 AC XY: 3520 AN XY: 33762

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.00730

Gnomad AMR AF: 0.0636

Gnomad ASJ AF: 0.0907

Gnomad EAS AF: 0.00447

Gnomad SAS AF: 0.0509

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.113

Gnomad NFE AF: 0.0943

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.114 AC: 12725 AN: 111600 Hom.: 649 Cov.: 22 AF XY: 0.104 AC XY: 3530 AN XY: 33828

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.0635

Gnomad4 ASJ AF: 0.0907

Gnomad4 EAS AF: 0.00448

Gnomad4 SAS AF: 0.0510

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0943

Gnomad4 OTH AF: 0.0927

Alfa AF: 0.0959 Hom.: 4698

Bravo AF: 0.114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5971535; hg19: chrX-31013090;