4-133565856-G-C

Variant names:

• chr4-133565856-G-C
• rs9307696

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 0.662 in 152,036 control chromosomes in the GnomAD database, including 33,690 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 0.66 (33690 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.747 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: 0.661 AC: 100477 AN: 151916 Hom.: 33640 Cov.: 32

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.627

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.662 AC: 100583 AN: 152036 Hom.: 33690 Cov.: 32 AF XY: 0.659 AC XY: 49008 AN XY: 74316

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.728

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.627

Gnomad4 OTH AF: 0.625

Alfa AF: 0.517 Hom.: 1419

Bravo AF: 0.663

Asia WGS AF: 0.639 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9307696; hg19: chr4-134487011;