rs1554027

Variant names:

• chr3-96310479-G-C
• rs1554027

Your query was ambiguous. Multiple possible variants found:

• chr3-96310479-G-C
• chr3-96310479-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 0.627 in 151,606 control chromosomes in the GnomAD database, including 30,615 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 0.63 (30615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.801 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: 0.627 AC: 95033 AN: 151486 Hom.: 30572 Cov.: 32

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.822

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.627 AC: 95132 AN: 151606 Hom.: 30615 Cov.: 32 AF XY: 0.631 AC XY: 46752 AN XY: 74064

African (AFR) AF: 0.759 AC: 31483 AN: 41458

American (AMR) AF: 0.581 AC: 8816 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1563 AN: 3462

East Asian (EAS) AF: 0.822 AC: 4234 AN: 5150

South Asian (SAS) AF: 0.690 AC: 3326 AN: 4822

European-Finnish (FIN) AF: 0.612 AC: 6441 AN: 10530

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.551 AC: 37323 AN: 67698

Other (OTH) AF: 0.604 AC: 1270 AN: 2104

Alfa AF: 0.501 Hom.: 1561

Bravo AF: 0.632

Asia WGS AF: 0.787 AC: 2721 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.59
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs1554027; hg19: chr3-96029323;