rs551284

Variant names:

• chr1-103941785-A-G
• rs551284

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 0.3 in 151,868 control chromosomes in the GnomAD database, including 7,144 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 0.30 (7144 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.351 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: 0.300 AC: 45528 AN: 151750 Hom.: 7138 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.300 AC: 45553 AN: 151868 Hom.: 7144 Cov.: 32 AF XY: 0.299 AC XY: 22202 AN XY: 74244

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.318

Alfa AF: 0.338 Hom.: 6888

Bravo AF: 0.303

Asia WGS AF: 0.322 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.16
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs551284; hg19: chr1-104484407;