rs11204553

Variant names:

• chr1-247906610-G-A
• rs11204553

Your query was ambiguous. Multiple possible variants found:

• chr1-247906610-G-A
• chr1-247906610-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 0.734 in 152,090 control chromosomes in the GnomAD database, including 42,348 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 0.73 (42348 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.05
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 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: 0.734 AC: 111571 AN: 151972 Hom.: 42351 Cov.: 33

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.831

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.734 AC: 111609 AN: 152090 Hom.: 42348 Cov.: 33 AF XY: 0.734 AC XY: 54571 AN XY: 74346

African (AFR) AF: 0.526 AC: 21799 AN: 41438

American (AMR) AF: 0.747 AC: 11418 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.831 AC: 2882 AN: 3468

East Asian (EAS) AF: 0.969 AC: 5022 AN: 5180

South Asian (SAS) AF: 0.712 AC: 3429 AN: 4816

European-Finnish (FIN) AF: 0.837 AC: 8859 AN: 10578

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55632 AN: 68012

Other (OTH) AF: 0.765 AC: 1616 AN: 2112

Alfa AF: 0.798 Hom.: 78162

Bravo AF: 0.726

Asia WGS AF: 0.835 AC: 2902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.94
DANN	Benign	0.75
PhyloP100		-4.1

Splicing

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

Other links and lift over

dbSNP: rs11204553; hg19: chr1-248069912;