chr11-102707818-C-T

Variant names:

• chr11-102707818-C-T
• rs12361599

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 0.179 in 152,062 control chromosomes in the GnomAD database, including 3,134 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 0.18 (3134 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 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: 0.179 AC: 27173 AN: 151944 Hom.: 3131 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.0913

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.179 AC: 27172 AN: 152062 Hom.: 3134 Cov.: 32 AF XY: 0.177 AC XY: 13188 AN XY: 74334

African (AFR) AF: 0.0473 AC: 1963 AN: 41496

American (AMR) AF: 0.190 AC: 2908 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 624 AN: 3470

East Asian (EAS) AF: 0.0915 AC: 474 AN: 5180

South Asian (SAS) AF: 0.149 AC: 718 AN: 4810

European-Finnish (FIN) AF: 0.249 AC: 2633 AN: 10572

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17267 AN: 67948

Other (OTH) AF: 0.158 AC: 335 AN: 2114

Alfa AF: 0.212 Hom.: 533

Bravo AF: 0.172

Asia WGS AF: 0.106 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.35
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs12361599; hg19: chr11-102578549; COSMIC: COSV52630851;