X-71199058-T-C

Variant names:

• chrX-71199058-T-C
• rs12396931

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.47 (9396 hom., 13429 hem., cov: 20)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.642 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: 0.465 AC: 50091 AN: 107735 Hom.: 9386 Cov.: 20

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.465 AC: 50133 AN: 107781 Hom.: 9396 Cov.: 20 AF XY: 0.443 AC XY: 13429 AN XY: 30323

African (AFR) AF: 0.650 AC: 19207 AN: 29549

American (AMR) AF: 0.354 AC: 3563 AN: 10078

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 1549 AN: 2601

East Asian (EAS) AF: 0.504 AC: 1669 AN: 3313

South Asian (SAS) AF: 0.454 AC: 1107 AN: 2441

European-Finnish (FIN) AF: 0.337 AC: 1845 AN: 5468

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

European-Non Finnish (NFE) AF: 0.385 AC: 20011 AN: 52004

Other (OTH) AF: 0.491 AC: 721 AN: 1469

Alfa AF: 0.212 Hom.: 891

Bravo AF: 0.478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.57
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs12396931; hg19: chrX-70418908;