1-55030366-T-C

Variant names:

• chr1-55030366-T-C
• rs11206510

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 283 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.137 AC: 5691 AN: 41554

American (AMR) AF: 0.110 AC: 1677 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 609 AN: 3472

East Asian (EAS) AF: 0.0492 AC: 255 AN: 5178

South Asian (SAS) AF: 0.0489 AC: 236 AN: 4828

European-Finnish (FIN) AF: 0.172 AC: 1821 AN: 10598

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12406 AN: 68018

Other (OTH) AF: 0.160 AC: 337 AN: 2110

Alfa AF: 0.170 Hom.: 10291

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

Mar 03, 2022

Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic

Significance: association

Review Status: no assertion criteria provided

Collection Method: research

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
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs11206510; hg19: chr1-55496039;