rs2055978

Variant names:

• chr3-146175504-C-T
• rs2055978

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 0.0452 in 152,110 control chromosomes in the GnomAD database, including 406 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 0.045 (406 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 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: 0.0451 AC: 6857 AN: 151994 Hom.: 406 Cov.: 33

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0214

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00724

Gnomad OTH AF: 0.0392

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

GnomAD4 genome AF: 0.0452 AC: 6870 AN: 152110 Hom.: 406 Cov.: 33 AF XY: 0.0444 AC XY: 3299 AN XY: 74368

African (AFR) AF: 0.138 AC: 5711 AN: 41474

American (AMR) AF: 0.0214 AC: 326 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0138 AC: 48 AN: 3470

East Asian (EAS) AF: 0.0205 AC: 106 AN: 5176

South Asian (SAS) AF: 0.0106 AC: 51 AN: 4820

European-Finnish (FIN) AF: 0.00245 AC: 26 AN: 10596

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

European-Non Finnish (NFE) AF: 0.00725 AC: 493 AN: 67992

Other (OTH) AF: 0.0393 AC: 83 AN: 2112

Alfa AF: 0.0342 Hom.: 53

Bravo AF: 0.0502

Asia WGS AF: 0.0350 AC: 123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.40
DANN	Benign	0.64
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2055978; hg19: chr3-145893291;