rs4420311

Variant names:

• chr12-27831257-G-A
• rs4420311

Your query was ambiguous. Multiple possible variants found:

• chr12-27831257-G-A
• chr12-27831257-G-C
• chr12-27831257-G-T

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 0.567 in 151,842 control chromosomes in the GnomAD database, including 24,530 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 0.57 (24530 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.595 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: 0.567 AC: 86048 AN: 151724 Hom.: 24516 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.567 AC: 86114 AN: 151842 Hom.: 24530 Cov.: 31 AF XY: 0.574 AC XY: 42588 AN XY: 74174

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.571

Alfa AF: 0.542 Hom.: 20657

Bravo AF: 0.564

Asia WGS AF: 0.592 AC: 2058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4420311; hg19: chr12-27984190;