chr4-180903867-G-A

Position:

• chr4-180903867-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 0.673 in 151,918 control chromosomes in the GnomAD database, including 34,743 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 0.67 (34743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493

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 = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102152 AN: 151798 Hom.: 34715 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.673 AC: 102216 AN: 151918 Hom.: 34743 Cov.: 32 AF XY: 0.683 AC XY: 50697 AN XY: 74234

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.674

Gnomad4 OTH AF: 0.657

Alfa AF: 0.676 Hom.: 14919

Bravo AF: 0.667

Asia WGS AF: 0.790 AC: 2749 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	0.80
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6845611; hg19: chr4-181825020;