4-180903867-G-A

Variant names:

• chr4-180903867-G-A
• rs6845611

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;