rs540224

Variant names:

• chr1-160793580-G-A
• rs540224

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 0.324 in 152,030 control chromosomes in the GnomAD database, including 8,126 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 0.32 (8126 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.447 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: 0.324 AC: 49171 AN: 151912 Hom.: 8115 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.324 AC: 49214 AN: 152030 Hom.: 8126 Cov.: 31 AF XY: 0.324 AC XY: 24050 AN XY: 74320

Gnomad4 AFR AF: 0.356

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.376

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.316

Alfa AF: 0.317 Hom.: 947

Bravo AF: 0.322

Asia WGS AF: 0.415 AC: 1446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.78
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs540224; hg19: chr1-160763370;