11-71553875-T-C

Variant names:

• chr11-71553875-T-C
• rs10898290

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 0.307 in 151,882 control chromosomes in the GnomAD database, including 7,545 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 0.31 (7545 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46670 AN: 151764 Hom.: 7540 Cov.: 31

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.307 AC: 46703 AN: 151882 Hom.: 7545 Cov.: 31 AF XY: 0.313 AC XY: 23235 AN XY: 74234

African (AFR) AF: 0.285 AC: 11819 AN: 41420

American (AMR) AF: 0.404 AC: 6170 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 630 AN: 3470

East Asian (EAS) AF: 0.517 AC: 2661 AN: 5146

South Asian (SAS) AF: 0.218 AC: 1052 AN: 4816

European-Finnish (FIN) AF: 0.368 AC: 3858 AN: 10496

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.287 AC: 19531 AN: 67954

Other (OTH) AF: 0.287 AC: 606 AN: 2110

Alfa AF: 0.169 Hom.: 315

Bravo AF: 0.316

Asia WGS AF: 0.325 AC: 1131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.30
DANN	Benign	0.18
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs10898290; hg19: chr11-71264921;