4-180308047-G-A

Position:

• chr4-180308047-G-A

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 0.132 in 151,986 control chromosomes in the GnomAD database, including 1,397 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 0.13 (1397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 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: 0.132 AC: 20023 AN: 151866 Hom.: 1400 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.132 AC: 20017 AN: 151986 Hom.: 1397 Cov.: 32 AF XY: 0.132 AC XY: 9778 AN XY: 74250

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.116

Alfa AF: 0.133 Hom.: 567

Bravo AF: 0.129

Asia WGS AF: 0.158 AC: 547 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.89
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17834666; hg19: chr4-181229200;