rs1402405

chr6-24090269-G-Achr6-24090269-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 0.546 in 152,018 control chromosomes in the GnomAD database, including 22,805 homozygotes. 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 0.55 (22805 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.835

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.626 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: 0.546 AC: 82931 AN: 151900 Hom.: 22790 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.546 AC: 82974 AN: 152018 Hom.: 22805 Cov.: 32 AF XY: 0.544 AC XY: 40405 AN XY: 74326

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.526

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.570

Alfa AF: 0.549 Hom.: 44156

Bravo AF: 0.546

Asia WGS AF: 0.574 AC: 1994 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.21
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402405; hg19: chr6-24090497;