4-118028335-T-C

Variant names:

• chr4-118028335-T-C
• rs2389493

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 0.748 in 152,094 control chromosomes in the GnomAD database, including 44,438 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 0.75 (44438 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.520
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113747 AN: 151976 Hom.: 44404 Cov.: 33

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.899

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.748 AC: 113831 AN: 152094 Hom.: 44438 Cov.: 33 AF XY: 0.752 AC XY: 55905 AN XY: 74342

African (AFR) AF: 0.509 AC: 21109 AN: 41432

American (AMR) AF: 0.821 AC: 12547 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2805 AN: 3470

East Asian (EAS) AF: 0.747 AC: 3864 AN: 5172

South Asian (SAS) AF: 0.899 AC: 4347 AN: 4834

European-Finnish (FIN) AF: 0.821 AC: 8685 AN: 10584

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57946 AN: 68002

Other (OTH) AF: 0.746 AC: 1576 AN: 2114

Alfa AF: 0.793 Hom.: 6807

Bravo AF: 0.732

Asia WGS AF: 0.821 AC: 2854 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.65
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs2389493; hg19: chr4-118949490;