3-31086419-T-C

Position:

• chr3-31086419-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 0.425 in 152,042 control chromosomes in the GnomAD database, including 15,494 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 0.43 (15494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64594 AN: 151924 Hom.: 15482 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.425 AC: 64634 AN: 152042 Hom.: 15494 Cov.: 32 AF XY: 0.422 AC XY: 31378 AN XY: 74350

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.456

Gnomad4 EAS AF: 0.378

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.458

Alfa AF: 0.496 Hom.: 10354

Bravo AF: 0.397

Asia WGS AF: 0.388 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	6.1
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs294278; hg19: chr3-31127911;