chr11-98902167-C-T

Variant names:

• chr11-98902167-C-T
• rs11217465

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 0.273 in 151,890 control chromosomes in the GnomAD database, including 6,529 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 0.27 (6529 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41391 AN: 151772 Hom.: 6525 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.273 AC: 41400 AN: 151890 Hom.: 6529 Cov.: 32 AF XY: 0.283 AC XY: 20973 AN XY: 74230

African (AFR) AF: 0.144 AC: 5987 AN: 41458

American (AMR) AF: 0.421 AC: 6409 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 996 AN: 3460

East Asian (EAS) AF: 0.250 AC: 1287 AN: 5158

South Asian (SAS) AF: 0.448 AC: 2158 AN: 4816

European-Finnish (FIN) AF: 0.388 AC: 4091 AN: 10546

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19610 AN: 67902

Other (OTH) AF: 0.256 AC: 541 AN: 2110

Alfa AF: 0.286 Hom.: 10648

Bravo AF: 0.267

Asia WGS AF: 0.344 AC: 1194 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.55
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11217465; hg19: chr11-98772897;