chr1-55030366-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: 286 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

ClinVar submissions

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Familial hypercholesterolemia (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-2.8

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11206510; hg19: chr1-55496039;