rs1546766

Variant names:

• chr1-79791769-A-T
• rs1546766

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 0.484 in 152,048 control chromosomes in the GnomAD database, including 18,590 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 0.48 (18590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.548 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: 0.484 AC: 73563 AN: 151930 Hom.: 18589 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.532

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.484 AC: 73602 AN: 152048 Hom.: 18590 Cov.: 32 AF XY: 0.489 AC XY: 36363 AN XY: 74318

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.532

Gnomad4 OTH AF: 0.513

Alfa AF: 0.498 Hom.: 2451

Bravo AF: 0.474

Asia WGS AF: 0.479 AC: 1663 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.55
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1546766; hg19: chr1-80257454; COSMIC: COSV59960489;