rs16844489

Variant names:

• chr3-137093276-T-C
• rs16844489

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 0.0582 in 152,314 control chromosomes in the GnomAD database, including 300 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 0.058 (300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.123 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: 0.0582 AC: 8859 AN: 152198 Hom.: 300 Cov.: 32

Gnomad AFR AF: 0.0337

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.0431

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0673

Gnomad FIN AF: 0.0700

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0689

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0582 AC: 8859 AN: 152314 Hom.: 300 Cov.: 32 AF XY: 0.0590 AC XY: 4391 AN XY: 74470

African (AFR) AF: 0.0336 AC: 1397 AN: 41574

American (AMR) AF: 0.0430 AC: 658 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0435 AC: 151 AN: 3472

East Asian (EAS) AF: 0.131 AC: 679 AN: 5190

South Asian (SAS) AF: 0.0672 AC: 324 AN: 4824

European-Finnish (FIN) AF: 0.0700 AC: 742 AN: 10604

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0690 AC: 4691 AN: 68030

Other (OTH) AF: 0.0563 AC: 119 AN: 2114

Alfa AF: 0.0638 Hom.: 41

Bravo AF: 0.0542

Asia WGS AF: 0.110 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.39
DANN	Benign	0.94
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs16844489; hg19: chr3-136812118;