rs1478829

chr6-120239548-T-Achr6-120239548-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 0.565 in 151,790 control chromosomes in the GnomAD database, including 24,352 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 0.56 (24352 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 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: 0.565 AC: 85692 AN: 151674 Hom.: 24332 Cov.: 30

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.565 AC: 85752 AN: 151790 Hom.: 24352 Cov.: 30 AF XY: 0.566 AC XY: 41972 AN XY: 74160

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.590

Alfa AF: 0.567 Hom.: 2896

Bravo AF: 0.564

Asia WGS AF: 0.564 AC: 1962 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.9
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: rs1478829; hg19: chr6-120560694;