chr4-83759773-T-C

Variant names:

• chr4-83759773-T-C
• rs1379981

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.702 in 152,138 control chromosomes in the GnomAD database, including 37,840 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 0.70 (37840 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.889
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.868 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: 0.702 AC: 106746 AN: 152020 Hom.: 37795 Cov.: 33

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.809

Gnomad AMR AF: 0.743

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.843

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.702 AC: 106852 AN: 152138 Hom.: 37840 Cov.: 33 AF XY: 0.703 AC XY: 52289 AN XY: 74364

African (AFR) AF: 0.627 AC: 26017 AN: 41502

American (AMR) AF: 0.744 AC: 11369 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2212 AN: 3470

East Asian (EAS) AF: 0.890 AC: 4605 AN: 5176

South Asian (SAS) AF: 0.844 AC: 4071 AN: 4822

European-Finnish (FIN) AF: 0.680 AC: 7187 AN: 10574

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49097 AN: 67984

Other (OTH) AF: 0.661 AC: 1398 AN: 2114

Alfa AF: 0.720 Hom.: 13348

Bravo AF: 0.699

Asia WGS AF: 0.881 AC: 3059 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	22
DANN	Benign	0.72
PhyloP100		0.89

Splicing

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

Other links and lift over

dbSNP: rs1379981; hg19: chr4-84680926;