rs551284

Positions:

• chr1-103941785-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 0.3 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;