rs4664789

Variant names:

• chr2-156011024-C-A
• rs4664789

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.459 in 151,924 control chromosomes in the GnomAD database, including 16,299 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 0.46 (16299 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.647

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.527 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: 0.459 AC: 69679 AN: 151806 Hom.: 16284 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.459 AC: 69719 AN: 151924 Hom.: 16299 Cov.: 32 AF XY: 0.456 AC XY: 33840 AN XY: 74244

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.472

Alfa AF: 0.490 Hom.: 8441

Bravo AF: 0.468

Asia WGS AF: 0.407 AC: 1418 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	5.3
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4664789; hg19: chr2-156867536;