chr3-110317781-A-G

Variant names:

• chr3-110317781-A-G
• rs12639225

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 0.402 in 152,092 control chromosomes in the GnomAD database, including 13,782 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 0.40 (13782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 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: 0.402 AC: 61076 AN: 151974 Hom.: 13776 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.402 AC: 61111 AN: 152092 Hom.: 13782 Cov.: 32 AF XY: 0.409 AC XY: 30374 AN XY: 74334

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.249

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.442

Alfa AF: 0.467 Hom.: 9234

Bravo AF: 0.374

Asia WGS AF: 0.404 AC: 1406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12639225; hg19: chr3-110036628;