4-125085266-T-C

Variant names:

• chr4-125085266-T-C
• rs7699788

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.783 in 152,128 control chromosomes in the GnomAD database, including 47,325 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 0.78 (47325 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.857 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: 0.784 AC: 119134 AN: 152012 Hom.: 47309 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.784

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.783 AC: 119190 AN: 152128 Hom.: 47325 Cov.: 32 AF XY: 0.779 AC XY: 57893 AN XY: 74358

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.786

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.787

Alfa AF: 0.820 Hom.: 7147

Bravo AF: 0.773

Asia WGS AF: 0.700 AC: 2430 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.4
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7699788; hg19: chr4-126006421;