rs6426833

chr1-19845367-G-Achr1-19845367-G-Cchr1-19845367-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 0.522 in 152,114 control chromosomes in the GnomAD database, including 21,086 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 0.52 (21086 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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: 0.522 AC: 79384 AN: 151994 Hom.: 21087 Cov.: 34

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.697

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.522 AC: 79409 AN: 152114 Hom.: 21086 Cov.: 34 AF XY: 0.523 AC XY: 38904 AN XY: 74354

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.539

Alfa AF: 0.546 Hom.: 49127

Bravo AF: 0.516

Asia WGS AF: 0.699 AC: 2429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.8
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6426833; hg19: chr1-20171860;