rs2897404

Positions:

• chrX-10380285-C-T

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 0.325 in 111,267 control chromosomes in the GnomAD database, including 4,558 homozygotes. There are 11,210 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 0.32 (4558 hom., 11210 hem., cov: 24)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.10380285C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.325 AC: 36159 AN: 111212 Hom.: 4560 Cov.: 24 AF XY: 0.334 AC XY: 11199 AN XY: 33518

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.325 AC: 36160 AN: 111267 Hom.: 4558 Cov.: 24 AF XY: 0.334 AC XY: 11210 AN XY: 33583

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.342

Alfa AF: 0.315 Hom.: 2234

Bravo AF: 0.340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2897404; hg19: chrX-10348325;