3-86109735-C-T

Variant names:

• chr3-86109735-C-T
• rs2324999

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 0.215 in 152,096 control chromosomes in the GnomAD database, including 3,543 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 0.21 (3543 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.269 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: 0.215 AC: 32621 AN: 151978 Hom.: 3545 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.215 AC: 32627 AN: 152096 Hom.: 3543 Cov.: 33 AF XY: 0.217 AC XY: 16091 AN XY: 74322

African (AFR) AF: 0.233 AC: 9672 AN: 41468

American (AMR) AF: 0.211 AC: 3220 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 875 AN: 3472

East Asian (EAS) AF: 0.218 AC: 1125 AN: 5160

South Asian (SAS) AF: 0.281 AC: 1357 AN: 4824

European-Finnish (FIN) AF: 0.192 AC: 2032 AN: 10568

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13644 AN: 68006

Other (OTH) AF: 0.216 AC: 456 AN: 2116

Alfa AF: 0.206 Hom.: 6845

Bravo AF: 0.214

Asia WGS AF: 0.252 AC: 872 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2324999; hg19: chr3-86158885;