rs1972809

chrX-120733621-A-G

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 0.467 in 110,620 control chromosomes in the GnomAD database, including 9,038 homozygotes. There are 15,084 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 0.47 (9038 hom., 15084 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.467 AC: 51644 AN: 110566 Hom.: 9040 Cov.: 22 AF XY: 0.458 AC XY: 15039 AN XY: 32810

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.460

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.467 AC: 51687 AN: 110620 Hom.: 9038 Cov.: 22 AF XY: 0.459 AC XY: 15084 AN XY: 32874

Gnomad4 AFR AF: 0.610

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.459

Alfa AF: 0.448 Hom.: 3486

Bravo AF: 0.481

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.3
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1972809; hg19: chrX-119867475; COSMIC: COSV70204342;