chr4-40334583-T-A

Variant names:

• chr4-40334583-T-A
• rs6823439

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 0.593 in 151,768 control chromosomes in the GnomAD database, including 28,231 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 0.59 (28231 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.643
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 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: 0.593 AC: 89895 AN: 151648 Hom.: 28189 Cov.: 30

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.593 AC: 89990 AN: 151768 Hom.: 28231 Cov.: 30 AF XY: 0.588 AC XY: 43611 AN XY: 74146

African (AFR) AF: 0.797 AC: 32965 AN: 41366

American (AMR) AF: 0.580 AC: 8854 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1646 AN: 3470

East Asian (EAS) AF: 0.203 AC: 1051 AN: 5174

South Asian (SAS) AF: 0.401 AC: 1929 AN: 4812

European-Finnish (FIN) AF: 0.557 AC: 5828 AN: 10472

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.526 AC: 35706 AN: 67910

Other (OTH) AF: 0.558 AC: 1177 AN: 2108

Alfa AF: 0.575 Hom.: 3199

Bravo AF: 0.603

Asia WGS AF: 0.335 AC: 1167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.73
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs6823439; hg19: chr4-40336600;