rs2497938

Positions:

• chrX-67343176-T-C

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 0.359 in 110,144 control chromosomes in the GnomAD database, including 9,190 homozygotes. There are 10,807 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 0.36 (9190 hom., 10807 hem., cov: 22)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.854 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.67343176T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.359 AC: 39530 AN: 110086 Hom.: 9182 Cov.: 22 AF XY: 0.332 AC XY: 10755 AN XY: 32360

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000857

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.359 AC: 39594 AN: 110144 Hom.: 9190 Cov.: 22 AF XY: 0.333 AC XY: 10807 AN XY: 32428

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.000860

Gnomad4 SAS AF: 0.0782

Gnomad4 FIN AF: 0.179

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.310

Alfa AF: 0.192 Hom.: 10203

Bravo AF: 0.379

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.13
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2497938; hg19: chrX-66563018;