11-80441288-T-C

Variant names:

• chr11-80441288-T-C
• rs2443951

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 0.28 in 151,966 control chromosomes in the GnomAD database, including 7,097 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 0.28 (7097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0530
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.372 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: 0.280 AC: 42581 AN: 151848 Hom.: 7093 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.0842

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.280 AC: 42596 AN: 151966 Hom.: 7097 Cov.: 32 AF XY: 0.278 AC XY: 20663 AN XY: 74248

African (AFR) AF: 0.121 AC: 5006 AN: 41450

American (AMR) AF: 0.211 AC: 3215 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1408 AN: 3466

East Asian (EAS) AF: 0.0844 AC: 436 AN: 5166

South Asian (SAS) AF: 0.307 AC: 1480 AN: 4816

European-Finnish (FIN) AF: 0.422 AC: 4447 AN: 10550

Middle Eastern (MID) AF: 0.303 AC: 88 AN: 290

European-Non Finnish (NFE) AF: 0.375 AC: 25514 AN: 67956

Other (OTH) AF: 0.291 AC: 613 AN: 2110

Alfa AF: 0.340 Hom.: 15530

Bravo AF: 0.256

Asia WGS AF: 0.205 AC: 713 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.71
PhyloP100		0.053

Splicing

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

Other links and lift over

dbSNP: rs2443951; hg19: chr11-80152332;