11-98595538-T-C

Variant names:

• chr11-98595538-T-C
• rs4237591

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 0.39 in 151,826 control chromosomes in the GnomAD database, including 11,817 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 0.39 (11817 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59162 AN: 151708 Hom.: 11809 Cov.: 31

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.448

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.390 AC: 59202 AN: 151826 Hom.: 11817 Cov.: 31 AF XY: 0.392 AC XY: 29073 AN XY: 74190

African (AFR) AF: 0.429 AC: 17772 AN: 41416

American (AMR) AF: 0.391 AC: 5964 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1050 AN: 3464

East Asian (EAS) AF: 0.447 AC: 2293 AN: 5126

South Asian (SAS) AF: 0.381 AC: 1840 AN: 4826

European-Finnish (FIN) AF: 0.397 AC: 4176 AN: 10522

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25039 AN: 67920

Other (OTH) AF: 0.359 AC: 758 AN: 2110

Alfa AF: 0.374 Hom.: 25069

Bravo AF: 0.392

Asia WGS AF: 0.417 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.7
DANN	Benign	0.48
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs4237591; hg19: chr11-98466268;