rs1551641

Variant names:

• chr4-55127748-C-T
• rs1551641

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 0.253 in 151,414 control chromosomes in the GnomAD database, including 5,242 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 0.25 (5242 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 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: 0.253 AC: 38282 AN: 151296 Hom.: 5244 Cov.: 29

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.253 AC: 38274 AN: 151414 Hom.: 5242 Cov.: 29 AF XY: 0.251 AC XY: 18540 AN XY: 73954

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.392

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.262

Alfa AF: 0.281 Hom.: 797

Bravo AF: 0.246

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	20
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1551641; hg19: chr4-55993915;