chr1-11340352-A-C

Variant names:

• chr1-11340352-A-C
• rs3120819

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 0.55 in 152,098 control chromosomes in the GnomAD database, including 23,810 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 0.55 (23810 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

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 (NFE) allele frequency at 95% confidence interval = 0.602 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: 0.550 AC: 83629 AN: 151980 Hom.: 23783 Cov.: 33

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.548

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

GnomAD4 genome AF: 0.550 AC: 83699 AN: 152098 Hom.: 23810 Cov.: 33 AF XY: 0.543 AC XY: 40381 AN XY: 74332

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.548

Alfa AF: 0.577 Hom.: 32538

Bravo AF: 0.531

Asia WGS AF: 0.359 AC: 1249 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	1.6
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3120819; hg19: chr1-11400409;