rs996106

Variant names:

• chrX-42962599-G-A
• rs996106

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 0.54 (11563 hom., 17348 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 0 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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: 0.535 AC: 58849 AN: 109983 Hom.: 11557 Cov.: 22

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.664

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.556

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.535 AC: 58877 AN: 110035 Hom.: 11563 Cov.: 22 AF XY: 0.536 AC XY: 17348 AN XY: 32347

African (AFR) AF: 0.376 AC: 11400 AN: 30321

American (AMR) AF: 0.665 AC: 6858 AN: 10319

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1395 AN: 2620

East Asian (EAS) AF: 0.716 AC: 2495 AN: 3484

South Asian (SAS) AF: 0.530 AC: 1359 AN: 2562

European-Finnish (FIN) AF: 0.635 AC: 3652 AN: 5748

Middle Eastern (MID) AF: 0.616 AC: 130 AN: 211

European-Non Finnish (NFE) AF: 0.581 AC: 30540 AN: 52587

Other (OTH) AF: 0.556 AC: 838 AN: 1506

Alfa AF: 0.573 Hom.: 34505

Bravo AF: 0.538

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs996106; hg19: chrX-42821848;