rs4023915

Variant names:

• chr16-86033783-G-C
• rs4023915

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 0.0935 in 152,272 control chromosomes in the GnomAD database, including 1,596 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 0.094 (1596 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.916
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 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: 0.0932 AC: 14188 AN: 152154 Hom.: 1578 Cov.: 34

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0834

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0113

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00617

Gnomad OTH AF: 0.0669

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

GnomAD4 genome AF: 0.0935 AC: 14239 AN: 152272 Hom.: 1596 Cov.: 34 AF XY: 0.0949 AC XY: 7063 AN XY: 74462

African (AFR) AF: 0.255 AC: 10599 AN: 41518

American (AMR) AF: 0.0832 AC: 1273 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0222 AC: 77 AN: 3472

East Asian (EAS) AF: 0.177 AC: 916 AN: 5180

South Asian (SAS) AF: 0.137 AC: 663 AN: 4822

European-Finnish (FIN) AF: 0.0113 AC: 120 AN: 10624

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.00619 AC: 421 AN: 68034

Other (OTH) AF: 0.0742 AC: 157 AN: 2116

Alfa AF: 0.0530 Hom.: 124

Bravo AF: 0.103

Asia WGS AF: 0.196 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.32
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs4023915; hg19: chr16-86067389;