rs11862306

Variant names:

• chr16-3011927-T-C
• rs11862306

Your query was ambiguous. Multiple possible variants found:

• chr16-3011927-T-C
• chr16-3011927-T-G

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 0.227 in 152,194 control chromosomes in the GnomAD database, including 4,383 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 0.23 (4383 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0480
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 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: 0.227 AC: 34452 AN: 152076 Hom.: 4372 Cov.: 33

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.227 AC: 34491 AN: 152194 Hom.: 4383 Cov.: 33 AF XY: 0.233 AC XY: 17339 AN XY: 74414

African (AFR) AF: 0.263 AC: 10919 AN: 41536

American (AMR) AF: 0.294 AC: 4486 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3472

East Asian (EAS) AF: 0.410 AC: 2118 AN: 5166

South Asian (SAS) AF: 0.418 AC: 2021 AN: 4832

European-Finnish (FIN) AF: 0.164 AC: 1744 AN: 10610

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.174 AC: 11820 AN: 67988

Other (OTH) AF: 0.238 AC: 503 AN: 2112

Alfa AF: 0.185 Hom.: 3571

Bravo AF: 0.234

Asia WGS AF: 0.445 AC: 1551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.4
DANN	Benign	0.42
PhyloP100		0.048

Splicing

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

Other links and lift over

dbSNP: rs11862306; hg19: chr16-3061928; COSMIC: COSV60911869;