rs545731

chr1-156141499-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;