3-31404307-C-T

Variant names:

• chr3-31404307-C-T
• rs9880831

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 0.429 in 151,412 control chromosomes in the GnomAD database, including 15,337 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 (15337 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.617 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: 0.429 AC: 64915 AN: 151294 Hom.: 15310 Cov.: 30

Gnomad AFR AF: 0.623

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.429 AC: 64986 AN: 151412 Hom.: 15337 Cov.: 30 AF XY: 0.429 AC XY: 31682 AN XY: 73918

Gnomad4 AFR AF: 0.623

Gnomad4 AMR AF: 0.504

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.394

Alfa AF: 0.345 Hom.: 13011

Bravo AF: 0.455

Asia WGS AF: 0.435 AC: 1515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9880831; hg19: chr3-31445799;