rs5969041

Variant names:

• chrX-86988257-A-G
• rs5969041

Your query was ambiguous. Multiple possible variants found:

• chrX-86988257-A-G
• chrX-86988257-A-T

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 0.412 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.412 AC: 45358 AN: 110112 Hom.: 7089 Cov.: 22

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

African (AFR) AF: 0.518 AC: 15639 AN: 30168

American (AMR) AF: 0.513 AC: 5310 AN: 10351

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1127 AN: 2632

East Asian (EAS) AF: 0.190 AC: 656 AN: 3459

South Asian (SAS) AF: 0.296 AC: 761 AN: 2567

European-Finnish (FIN) AF: 0.332 AC: 1940 AN: 5847

Middle Eastern (MID) AF: 0.416 AC: 87 AN: 209

European-Non Finnish (NFE) AF: 0.362 AC: 19089 AN: 52766

Other (OTH) AF: 0.417 AC: 622 AN: 1490

Alfa AF: 0.355 Hom.: 6801

Bravo AF: 0.434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.6
DANN	Benign	0.51
PhyloP100		0.072

Splicing

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

Other links and lift over

dbSNP: rs5969041; hg19: chrX-86243260;