4-3440284-G-C

Variant names:

• chr4-3440284-G-C
• rs762861

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 0.302 in 151,988 control chromosomes in the GnomAD database, including 7,123 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 0.30 (7123 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45923 AN: 151870 Hom.: 7127 Cov.: 33

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.302 AC: 45943 AN: 151988 Hom.: 7123 Cov.: 33 AF XY: 0.305 AC XY: 22688 AN XY: 74292

African (AFR) AF: 0.333 AC: 13803 AN: 41460

American (AMR) AF: 0.334 AC: 5104 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1293 AN: 3470

East Asian (EAS) AF: 0.447 AC: 2291 AN: 5124

South Asian (SAS) AF: 0.442 AC: 2131 AN: 4816

European-Finnish (FIN) AF: 0.253 AC: 2677 AN: 10602

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17623 AN: 67920

Other (OTH) AF: 0.302 AC: 636 AN: 2108

Alfa AF: 0.280 Hom.: 756

Bravo AF: 0.310

Asia WGS AF: 0.400 AC: 1387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.55
DANN	Benign	0.32
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs762861; hg19: chr4-3442011;