3-521716-G-C

Variant names:

• chr3-521716-G-C
• rs4685846

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 0.581 in 151,948 control chromosomes in the GnomAD database, including 27,045 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 0.58 (27045 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.771 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: 0.581 AC: 88205 AN: 151828 Hom.: 26998 Cov.: 32

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.392

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.581 AC: 88317 AN: 151948 Hom.: 27045 Cov.: 32 AF XY: 0.575 AC XY: 42705 AN XY: 74252

African (AFR) AF: 0.778 AC: 32276 AN: 41492

American (AMR) AF: 0.484 AC: 7391 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 1360 AN: 3466

East Asian (EAS) AF: 0.350 AC: 1805 AN: 5162

South Asian (SAS) AF: 0.487 AC: 2339 AN: 4804

European-Finnish (FIN) AF: 0.505 AC: 5317 AN: 10530

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.529 AC: 35961 AN: 67924

Other (OTH) AF: 0.552 AC: 1166 AN: 2112

Alfa AF: 0.555 Hom.: 3049

Bravo AF: 0.589

Asia WGS AF: 0.480 AC: 1672 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.2
DANN	Benign	0.56
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs4685846; hg19: chr3-563399;