11-102518857-C-T

Variant names:

• chr11-102518857-C-T
• rs12184413

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 0.099 in 152,218 control chromosomes in the GnomAD database, including 962 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 0.099 (962 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.237 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: 0.0990 AC: 15063 AN: 152100 Hom.: 961 Cov.: 32

Gnomad AFR AF: 0.0237

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.247

Gnomad SAS AF: 0.0821

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0990 AC: 15069 AN: 152218 Hom.: 962 Cov.: 32 AF XY: 0.0989 AC XY: 7359 AN XY: 74424

African (AFR) AF: 0.0236 AC: 980 AN: 41558

American (AMR) AF: 0.140 AC: 2145 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3468

East Asian (EAS) AF: 0.248 AC: 1284 AN: 5180

South Asian (SAS) AF: 0.0828 AC: 399 AN: 4820

European-Finnish (FIN) AF: 0.123 AC: 1303 AN: 10594

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8255 AN: 67996

Other (OTH) AF: 0.0980 AC: 207 AN: 2112

Alfa AF: 0.113 Hom.: 1315

Bravo AF: 0.0997

Asia WGS AF: 0.136 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.087
DANN	Benign	0.27
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs12184413; hg19: chr11-102389588;