chr1-55030366-T-C

Position:

• chr1-55030366-T-C

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 0.153 in 152,264 control chromosomes in the GnomAD database, including 1,932 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.15 (1932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -2.82

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.18 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: 0.153 AC: 23270 AN: 152146 Hom.: 1930 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0489

Gnomad SAS AF: 0.0482

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.153 AC: 23292 AN: 152264 Hom.: 1932 Cov.: 32 AF XY: 0.149 AC XY: 11092 AN XY: 74448

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0492

Gnomad4 SAS AF: 0.0489

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.160

Alfa AF: 0.171 Hom.: 5307

Bravo AF: 0.154

Asia WGS AF: 0.0670 AC: 234 AN: 3478

ClinVar

Significance: association

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Familial hypercholesterolemia Other:1

association, no assertion criteria provided

research

Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic

Mar 03, 2022

Associated with elevated LDL cholesterol levels and early onset coronary artery disease, especially in men. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.23
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11206510; hg19: chr1-55496039;