chr1-163063552-A-C

Variant names:

• chr1-163063552-A-C
• rs951436

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 0.417 in 151,964 control chromosomes in the GnomAD database, including 14,238 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 0.42 (14238 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.488 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: 0.418 AC: 63403 AN: 151846 Hom.: 14249 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.417 AC: 63397 AN: 151964 Hom.: 14238 Cov.: 32 AF XY: 0.417 AC XY: 30968 AN XY: 74266

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.495

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.492

Gnomad4 OTH AF: 0.410

Alfa AF: 0.442 Hom.: 2021

Bravo AF: 0.413

Asia WGS AF: 0.361 AC: 1256 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	9.0
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs951436; hg19: chr1-163033342;