3-106314580-T-C

Variant names:

• chr3-106314580-T-C
• rs9873496

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 0.423 in 152,078 control chromosomes in the GnomAD database, including 13,823 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 0.42 (13823 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.515 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: 0.423 AC: 64211 AN: 151960 Hom.: 13796 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.423 AC: 64263 AN: 152078 Hom.: 13823 Cov.: 33 AF XY: 0.428 AC XY: 31789 AN XY: 74340

African (AFR) AF: 0.338 AC: 14030 AN: 41466

American (AMR) AF: 0.482 AC: 7370 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1305 AN: 3472

East Asian (EAS) AF: 0.361 AC: 1865 AN: 5168

South Asian (SAS) AF: 0.532 AC: 2570 AN: 4828

European-Finnish (FIN) AF: 0.472 AC: 4990 AN: 10574

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30733 AN: 67974

Other (OTH) AF: 0.433 AC: 913 AN: 2108

Alfa AF: 0.444 Hom.: 10984

Bravo AF: 0.416

Asia WGS AF: 0.472 AC: 1642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.46
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs9873496; hg19: chr3-106033427;