rs1546766

Positions:

• chr1-79791769-A-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 0.484 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.79791769A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;