rs6609257

Variant names:

• chrX-43753461-G-A
• rs6609257

Your query was ambiguous. Multiple possible variants found:

• chrX-43753461-G-A
• chrX-43753461-G-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 0.477 in 110,616 control chromosomes in the GnomAD database, including 9,732 homozygotes. There are 15,390 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 0.48 (9732 hom., 15390 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 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: 0.477 AC: 52721 AN: 110565 Hom.: 9740 Cov.: 22 AF XY: 0.468 AC XY: 15367 AN XY: 32817

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.511

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.477 AC: 52726 AN: 110616 Hom.: 9732 Cov.: 22 AF XY: 0.468 AC XY: 15390 AN XY: 32878

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.378

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.483

Alfa AF: 0.551 Hom.: 35739

Bravo AF: 0.469

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6609257; hg19: chrX-43612708;