4-3440284-G-C

Variant names:

• chr4-3440284-G-C
• rs762861

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 0.302 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.302 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

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.447

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.302

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs762861; hg19: chr4-3442011;