rs5971535

Variant names:

• chrX-30994973-G-A
• rs5971535

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.114 AC: 12720 AN: 111544 Hom.: 648 Cov.: 22

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

African (AFR) AF: 0.190 AC: 5805 AN: 30611

American (AMR) AF: 0.0635 AC: 671 AN: 10572

Ashkenazi Jewish (ASJ) AF: 0.0907 AC: 240 AN: 2646

East Asian (EAS) AF: 0.00448 AC: 16 AN: 3570

South Asian (SAS) AF: 0.0510 AC: 137 AN: 2685

European-Finnish (FIN) AF: 0.113 AC: 680 AN: 6002

Middle Eastern (MID) AF: 0.105 AC: 23 AN: 219

European-Non Finnish (NFE) AF: 0.0943 AC: 5008 AN: 53100

Other (OTH) AF: 0.0927 AC: 140 AN: 1510

Alfa AF: 0.0995 Hom.: 6923

Bravo AF: 0.114

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.0
DANN	Benign	0.73
PhyloP100		1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs5971535;

hg19: chrX-31013090;