rs11150675

Variant names:

• chr16-28969210-G-A
• rs11150675

Your query was ambiguous. Multiple possible variants found:

• chr16-28969210-G-A
• chr16-28969210-G-T

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 151,886 control chromosomes in the GnomAD database, including 6,784 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 (6784 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 19 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 (NFE) allele frequency at 95% confidence interval = 0.352 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: 41454 AN: 151768 Hom.: 6786 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.437

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.273 AC: 41441 AN: 151886 Hom.: 6784 Cov.: 31 AF XY: 0.273 AC XY: 20241 AN XY: 74236

African (AFR) AF: 0.108 AC: 4498 AN: 41482

American (AMR) AF: 0.279 AC: 4257 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1421 AN: 3468

East Asian (EAS) AF: 0.148 AC: 763 AN: 5162

South Asian (SAS) AF: 0.122 AC: 584 AN: 4800

European-Finnish (FIN) AF: 0.437 AC: 4597 AN: 10524

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24191 AN: 67904

Other (OTH) AF: 0.306 AC: 644 AN: 2104

Alfa AF: 0.323 Hom.: 25440

Bravo AF: 0.258

Asia WGS AF: 0.126 AC: 445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.76
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs11150675; hg19: chr16-28980531;