chr4-40390108-T-A

Variant names:

• chr4-40390108-T-A
• rs278976

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 0.203 in 152,108 control chromosomes in the GnomAD database, including 3,226 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 0.20 (3226 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.337
• 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 = 0.22 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: 0.202 AC: 30765 AN: 151990 Hom.: 3210 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.203 AC: 30828 AN: 152108 Hom.: 3226 Cov.: 32 AF XY: 0.198 AC XY: 14716 AN XY: 74354

African (AFR) AF: 0.224 AC: 9298 AN: 41498

American (AMR) AF: 0.166 AC: 2531 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3468

East Asian (EAS) AF: 0.109 AC: 563 AN: 5184

South Asian (SAS) AF: 0.180 AC: 868 AN: 4828

European-Finnish (FIN) AF: 0.174 AC: 1839 AN: 10578

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14521 AN: 67972

Other (OTH) AF: 0.201 AC: 424 AN: 2112

Alfa AF: 0.202 Hom.: 411

Bravo AF: 0.202

Asia WGS AF: 0.150 AC: 523 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	5.6
DANN	Benign	0.40
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs278976; hg19: chr4-40392125;