3-188077869-T-C

Variant names:

• chr3-188077869-T-C
• rs2037184

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.441 in 152,120 control chromosomes in the GnomAD database, including 15,053 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 0.44 (15053 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

ACMG classification

Verdict is Benign. Variant got -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 = 0.594 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: 0.441 AC: 67057 AN: 152002 Hom.: 15038 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.480

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.441 AC: 67118 AN: 152120 Hom.: 15053 Cov.: 32 AF XY: 0.447 AC XY: 33279 AN XY: 74374

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.611

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.439

Alfa AF: 0.416 Hom.: 18753

Bravo AF: 0.443

Asia WGS AF: 0.638 AC: 2219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2037184; hg19: chr3-187795657;