chr16-11243864-G-T

Variant names:

• chr16-11243864-G-T
• rs11074956

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 0.34 in 152,054 control chromosomes in the GnomAD database, including 9,440 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 0.34 (9440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.956
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51737 AN: 151934 Hom.: 9440 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.340 AC: 51747 AN: 152054 Hom.: 9440 Cov.: 32 AF XY: 0.339 AC XY: 25179 AN XY: 74306

African (AFR) AF: 0.215 AC: 8926 AN: 41476

American (AMR) AF: 0.269 AC: 4106 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1441 AN: 3468

East Asian (EAS) AF: 0.305 AC: 1578 AN: 5180

South Asian (SAS) AF: 0.429 AC: 2064 AN: 4814

European-Finnish (FIN) AF: 0.408 AC: 4301 AN: 10550

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.414 AC: 28110 AN: 67980

Other (OTH) AF: 0.351 AC: 741 AN: 2114

Alfa AF: 0.387 Hom.: 17978

Bravo AF: 0.326

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.0
DANN	Benign	0.46
PhyloP100		0.96

Splicing

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

Other links and lift over

dbSNP: rs11074956; hg19: chr16-11337721; COSMIC: COSV73889163;