rs11803463

Variant names:

• chr1-242626064-T-C
• rs11803463

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 0.193 in 152,264 control chromosomes in the GnomAD database, including 3,012 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 0.19 (3012 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29362 AN: 152146 Hom.: 3012 Cov.: 33

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0809

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.193 AC: 29376 AN: 152264 Hom.: 3012 Cov.: 33 AF XY: 0.192 AC XY: 14302 AN XY: 74444

African (AFR) AF: 0.129 AC: 5364 AN: 41570

American (AMR) AF: 0.233 AC: 3570 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 921 AN: 3470

East Asian (EAS) AF: 0.0807 AC: 419 AN: 5190

South Asian (SAS) AF: 0.218 AC: 1051 AN: 4822

European-Finnish (FIN) AF: 0.188 AC: 1995 AN: 10604

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15280 AN: 67988

Other (OTH) AF: 0.212 AC: 448 AN: 2114

Alfa AF: 0.206 Hom.: 584

Bravo AF: 0.193

Asia WGS AF: 0.157 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.2
DANN	Benign	0.70
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11803463; hg19: chr1-242789366;