rs4308349

Variant names:

• chr4-154580961-G-A
• rs4308349

Your query was ambiguous. Multiple possible variants found:

• chr4-154580961-G-A
• chr4-154580961-G-C
• chr4-154580961-G-T

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 0.878 in 152,116 control chromosomes in the GnomAD database, including 58,599 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 0.88 (58599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 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: 0.878 AC: 133424 AN: 151998 Hom.: 58562 Cov.: 32

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.785

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.885

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

GnomAD4 genome AF: 0.878 AC: 133516 AN: 152116 Hom.: 58599 Cov.: 32 AF XY: 0.877 AC XY: 65193 AN XY: 74372

African (AFR) AF: 0.895 AC: 37158 AN: 41530

American (AMR) AF: 0.875 AC: 13373 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2724 AN: 3472

East Asian (EAS) AF: 0.943 AC: 4873 AN: 5168

South Asian (SAS) AF: 0.858 AC: 4136 AN: 4822

European-Finnish (FIN) AF: 0.852 AC: 8982 AN: 10546

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59331 AN: 67984

Other (OTH) AF: 0.884 AC: 1865 AN: 2110

Alfa AF: 0.872 Hom.: 42445

Bravo AF: 0.881

Asia WGS AF: 0.884 AC: 3064 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.37
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs4308349; hg19: chr4-155502113;