chr11-98980255-A-C

Variant names:

• chr11-98980255-A-C
• rs901540

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 0.483 in 151,954 control chromosomes in the GnomAD database, including 19,543 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 0.48 (19543 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.6 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: 0.483 AC: 73375 AN: 151836 Hom.: 19537 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.483 AC: 73396 AN: 151954 Hom.: 19543 Cov.: 32 AF XY: 0.488 AC XY: 36202 AN XY: 74246

African (AFR) AF: 0.251 AC: 10400 AN: 41482

American (AMR) AF: 0.605 AC: 9224 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1992 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1834 AN: 5150

South Asian (SAS) AF: 0.618 AC: 2978 AN: 4818

European-Finnish (FIN) AF: 0.601 AC: 6325 AN: 10530

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.573 AC: 38946 AN: 67936

Other (OTH) AF: 0.481 AC: 1012 AN: 2106

Alfa AF: 0.536 Hom.: 57534

Bravo AF: 0.468

Asia WGS AF: 0.473 AC: 1641 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.2
DANN	Benign	0.77
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs901540; hg19: chr11-98850985;