rs545731

Variant names:

• chr1-156141499-G-A
• rs545731

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 0.109 in 152,202 control chromosomes in the GnomAD database, including 1,396 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 0.11 (1396 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.500

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 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: 0.109 AC: 16560 AN: 152084 Hom.: 1394 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.0690

Gnomad ASJ AF: 0.0972

Gnomad EAS AF: 0.000773

Gnomad SAS AF: 0.0532

Gnomad FIN AF: 0.0372

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0676

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.109 AC: 16576 AN: 152202 Hom.: 1396 Cov.: 32 AF XY: 0.106 AC XY: 7918 AN XY: 74414

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.0688

Gnomad4 ASJ AF: 0.0972

Gnomad4 EAS AF: 0.000775

Gnomad4 SAS AF: 0.0533

Gnomad4 FIN AF: 0.0372

Gnomad4 NFE AF: 0.0676

Gnomad4 OTH AF: 0.0993

Alfa AF: 0.0917 Hom.: 117

Bravo AF: 0.116

Asia WGS AF: 0.0400 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.0
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs545731; hg19: chr1-156111290;