rs11865472

chr16-1134967-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.42 in 152,146 control chromosomes in the GnomAD database, including 14,410 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 0.42 (14410 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.842

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63833 AN: 152028 Hom.: 14414 Cov.: 34

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.498

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.420 AC: 63848 AN: 152146 Hom.: 14410 Cov.: 34 AF XY: 0.416 AC XY: 30951 AN XY: 74380

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.640

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.498

Gnomad4 OTH AF: 0.456

Alfa AF: 0.496 Hom.: 24781

Bravo AF: 0.404

Asia WGS AF: 0.330 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.8
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11865472; hg19: chr16-1184967;