chr4-124883324-T-C

Variant names:

• chr4-124883324-T-C
• rs1395326

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 0.792 in 152,088 control chromosomes in the GnomAD database, including 48,198 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 0.79 (48198 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 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: 0.792 AC: 120387 AN: 151968 Hom.: 48166 Cov.: 33

Gnomad AFR AF: 0.701

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.792 AC: 120470 AN: 152088 Hom.: 48198 Cov.: 33 AF XY: 0.787 AC XY: 58468 AN XY: 74338

African (AFR) AF: 0.701 AC: 29085 AN: 41494

American (AMR) AF: 0.803 AC: 12252 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3106 AN: 3472

East Asian (EAS) AF: 0.680 AC: 3504 AN: 5150

South Asian (SAS) AF: 0.757 AC: 3652 AN: 4826

European-Finnish (FIN) AF: 0.731 AC: 7731 AN: 10570

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.859 AC: 58420 AN: 67990

Other (OTH) AF: 0.822 AC: 1737 AN: 2114

Alfa AF: 0.851 Hom.: 57452

Bravo AF: 0.793

Asia WGS AF: 0.720 AC: 2496 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.86
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1395326; hg19: chr4-125804479;