rs1351109

Positions:

• chr3-81324666-G-A

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 0.4 in 152,060 control chromosomes in the GnomAD database, including 13,617 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 (13617 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

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 (AFR) allele frequency at 95% confidence interval = 0.603 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: 0.399 AC: 60678 AN: 151942 Hom.: 13580 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.400 AC: 60754 AN: 152060 Hom.: 13617 Cov.: 32 AF XY: 0.396 AC XY: 29405 AN XY: 74340

Gnomad4 AFR AF: 0.609

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.405

Alfa AF: 0.365 Hom.: 1385

Bravo AF: 0.412

Asia WGS AF: 0.391 AC: 1364 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	0.88
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1351109; hg19: chr3-81373817;