4-180903867-G-A

Variant names:

• chr4-180903867-G-A
• rs6845611

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.598 AC: 24767 AN: 41400

American (AMR) AF: 0.739 AC: 11283 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2040 AN: 3468

East Asian (EAS) AF: 0.786 AC: 4053 AN: 5158

South Asian (SAS) AF: 0.805 AC: 3884 AN: 4822

European-Finnish (FIN) AF: 0.761 AC: 8020 AN: 10540

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45818 AN: 67942

Other (OTH) AF: 0.657 AC: 1383 AN: 2104

Alfa AF: 0.676 Hom.: 16653

Bravo AF: 0.667

Asia WGS AF: 0.790 AC: 2749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.80
DANN	Benign	0.83
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs6845611; hg19: chr4-181825020;