rs1211304

Variant names:

• chr13-49806880-G-A
• rs1211304

Your query was ambiguous. Multiple possible variants found:

• chr13-49806880-G-A
• chr13-49806880-G-T

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 152,042 control chromosomes in the GnomAD database, including 2,092 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 0.15 (2092 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.233 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: 0.153 AC: 23278 AN: 151922 Hom.: 2090 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.0752

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.153 AC: 23296 AN: 152042 Hom.: 2092 Cov.: 32 AF XY: 0.152 AC XY: 11275 AN XY: 74330

African (AFR) AF: 0.237 AC: 9822 AN: 41432

American (AMR) AF: 0.115 AC: 1759 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3468

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5186

South Asian (SAS) AF: 0.0751 AC: 361 AN: 4810

European-Finnish (FIN) AF: 0.158 AC: 1672 AN: 10556

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8558 AN: 67992

Other (OTH) AF: 0.161 AC: 339 AN: 2112

Alfa AF: 0.128 Hom.: 687

Bravo AF: 0.152

Asia WGS AF: 0.0550 AC: 195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.23
DANN	Benign	0.65
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1211304; hg19: chr13-50381016;