rs4420311

Variant names:

• chr12-27831257-G-A
• rs4420311
• ENST00000825469.1:n.320+20167G>A

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. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000825469.1(ENSG00000257042):​n.320+20167G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000257042 ENST00000825469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 10 publications found

Genes affected

ENSG00000257042 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000257042	ENST00000825469.1	n.320+20167G>A		intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825470.1	n.175+20167G>A		intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825471.1	n.140+20167G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.583 AC: 24097 AN: 41366

American (AMR) AF: 0.584 AC: 8919 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2088 AN: 3466

East Asian (EAS) AF: 0.552 AC: 2850 AN: 5166

South Asian (SAS) AF: 0.614 AC: 2951 AN: 4808

European-Finnish (FIN) AF: 0.598 AC: 6293 AN: 10522

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36967 AN: 67934

Other (OTH) AF: 0.571 AC: 1207 AN: 2114

Alfa AF: 0.548 Hom.: 60349

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
PhyloP100		0.091

Splicing

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

Other links and lift over

dbSNP: rs4420311; hg19: chr12-27984190;