rs1540052

Positions:

• chr4-102216820-A-G

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 0.218 in 152,052 control chromosomes in the GnomAD database, including 4,144 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 0.22 (4144 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.804

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.375 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: 0.218 AC: 33163 AN: 151934 Hom.: 4134 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.218 AC: 33190 AN: 152052 Hom.: 4144 Cov.: 32 AF XY: 0.222 AC XY: 16519 AN XY: 74310

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.190

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.214

Alfa AF: 0.252 Hom.: 10386

Bravo AF: 0.200

Asia WGS AF: 0.279 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.9
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1540052; hg19: chr4-103137977;