chr16-86509435-A-G

Variant names:

• chr16-86509435-A-G
• rs1424019

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 0.688 in 152,220 control chromosomes in the GnomAD database, including 37,208 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 0.69 (37208 hom., cov: 36)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 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: 0.688 AC: 104663 AN: 152102 Hom.: 37181 Cov.: 36

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.779

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.688 AC: 104744 AN: 152220 Hom.: 37208 Cov.: 36 AF XY: 0.692 AC XY: 51536 AN XY: 74422

African (AFR) AF: 0.497 AC: 20634 AN: 41536

American (AMR) AF: 0.804 AC: 12301 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2734 AN: 3472

East Asian (EAS) AF: 0.865 AC: 4458 AN: 5156

South Asian (SAS) AF: 0.678 AC: 3278 AN: 4832

European-Finnish (FIN) AF: 0.779 AC: 8271 AN: 10614

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50727 AN: 67984

Other (OTH) AF: 0.723 AC: 1526 AN: 2112

Alfa AF: 0.702 Hom.: 4920

Bravo AF: 0.686

Asia WGS AF: 0.755 AC: 2623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.1
DANN	Benign	0.52
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1424019; hg19: chr16-86543041;