4-39783656-T-C

Variant names:

• chr4-39783656-T-C
• rs4263408

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 0.504 in 151,886 control chromosomes in the GnomAD database, including 20,156 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 0.50 (20156 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.617 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: 0.505 AC: 76579 AN: 151766 Hom.: 20137 Cov.: 31

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.504 AC: 76624 AN: 151886 Hom.: 20156 Cov.: 31 AF XY: 0.506 AC XY: 37542 AN XY: 74234

African (AFR) AF: 0.348 AC: 14412 AN: 41388

American (AMR) AF: 0.625 AC: 9528 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1830 AN: 3472

East Asian (EAS) AF: 0.635 AC: 3281 AN: 5170

South Asian (SAS) AF: 0.623 AC: 3000 AN: 4816

European-Finnish (FIN) AF: 0.508 AC: 5359 AN: 10544

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37490 AN: 67944

Other (OTH) AF: 0.533 AC: 1126 AN: 2112

Alfa AF: 0.541 Hom.: 67141

Bravo AF: 0.505

Asia WGS AF: 0.637 AC: 2217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.1
DANN	Benign	0.75
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4263408; hg19: chr4-39785276;