chr16-86451525-G-A

Variant names:

• chr16-86451525-G-A
• rs11644988

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 0.081 in 152,214 control chromosomes in the GnomAD database, including 787 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 0.081 (787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.246 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: 0.0810 AC: 12317 AN: 152096 Hom.: 785 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0368

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.0299

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0489

Gnomad OTH AF: 0.0808

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

GnomAD4 genome AF: 0.0810 AC: 12332 AN: 152214 Hom.: 787 Cov.: 32 AF XY: 0.0784 AC XY: 5837 AN XY: 74434

African (AFR) AF: 0.152 AC: 6291 AN: 41522

American (AMR) AF: 0.0368 AC: 562 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0478 AC: 166 AN: 3472

East Asian (EAS) AF: 0.258 AC: 1334 AN: 5174

South Asian (SAS) AF: 0.0245 AC: 118 AN: 4824

European-Finnish (FIN) AF: 0.0299 AC: 317 AN: 10600

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0488 AC: 3321 AN: 68014

Other (OTH) AF: 0.0804 AC: 170 AN: 2114

Alfa AF: 0.0938 Hom.: 357

Bravo AF: 0.0875

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs11644988; hg19: chr16-86485131;