3-154998568-T-C

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 0.449 in 152,060 control chromosomes in the GnomAD database, including 18,449 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 0.45 (18449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68306 AN: 151942 Hom.: 18450 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.449 AC: 68310 AN: 152060 Hom.: 18449 Cov.: 32 AF XY: 0.449 AC XY: 33386 AN XY: 74334

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.391

Gnomad4 FIN AF: 0.576

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.505

Alfa AF: 0.558 Hom.: 24549

Bravo AF: 0.433

Asia WGS AF: 0.425 AC: 1478 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.2
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2314612; hg19: chr3-154716357;