chr4-107478889-G-C

Position:

• chr4-107478889-G-C

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 0.734 in 151,884 control chromosomes in the GnomAD database, including 41,038 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 0.73 (41038 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111370 AN: 151768 Hom.: 40994 Cov.: 30

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.734 AC: 111473 AN: 151884 Hom.: 41038 Cov.: 30 AF XY: 0.735 AC XY: 54507 AN XY: 74178

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.720

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.735

Alfa AF: 0.608 Hom.: 1680

Bravo AF: 0.736

Asia WGS AF: 0.831 AC: 2887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
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: rs4956103; hg19: chr4-108400046;