rs4843165

Variant names:

• chr16-86571435-C-T
• rs4843165

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 0.29 in 152,032 control chromosomes in the GnomAD database, including 6,729 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 0.29 (6729 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.458 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: 0.290 AC: 44078 AN: 151916 Hom.: 6706 Cov.: 32

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.290 AC: 44158 AN: 152032 Hom.: 6729 Cov.: 32 AF XY: 0.297 AC XY: 22057 AN XY: 74268

African (AFR) AF: 0.269 AC: 11171 AN: 41480

American (AMR) AF: 0.404 AC: 6163 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1129 AN: 3470

East Asian (EAS) AF: 0.474 AC: 2440 AN: 5146

South Asian (SAS) AF: 0.376 AC: 1804 AN: 4802

European-Finnish (FIN) AF: 0.310 AC: 3277 AN: 10556

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17150 AN: 67996

Other (OTH) AF: 0.280 AC: 591 AN: 2110

Alfa AF: 0.263 Hom.: 7059

Bravo AF: 0.299

Asia WGS AF: 0.392 AC: 1363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.85
DANN	Benign	0.61
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs4843165; hg19: chr16-86605041;