rs1478829

Variant names:

• chr6-120239548-T-A
• rs1478829

Your query was ambiguous. Multiple possible variants found:

• chr6-120239548-T-A
• chr6-120239548-T-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.531 AC: 21972 AN: 41400

American (AMR) AF: 0.571 AC: 8700 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2204 AN: 3466

East Asian (EAS) AF: 0.472 AC: 2427 AN: 5144

South Asian (SAS) AF: 0.584 AC: 2815 AN: 4822

European-Finnish (FIN) AF: 0.611 AC: 6389 AN: 10464

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39496 AN: 67940

Other (OTH) AF: 0.590 AC: 1241 AN: 2102

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
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1478829; hg19: chr6-120560694;