rs4421324

Variant names:

• chr8-94111828-A-G
• rs4421324
• ENST00000804339.1:n.81-32339A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-94111828-A-G
• chr8-94111828-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000804339.1(ENSG00000304524):​n.81-32339A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,242 control chromosomes in the GnomAD database, including 1,341 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 0.12 (1341 hom., cov: 33)
• Consequence: ENSG00000304524 ENST00000804339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.572
• Publications: 2 publications found

Genes affected

ENSG00000304524 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.215 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
ENSG00000304524	ENST00000804339.1	n.81-32339A>G		intron_variant	Intron 1 of 2
ENSG00000304524	ENST00000804340.1	n.194+31631A>G		intron_variant	Intron 1 of 2
ENSG00000304524	ENST00000804341.1	n.134+28507A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18541 AN: 152124 Hom.: 1333 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.225

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0855

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.122 AC: 18573 AN: 152242 Hom.: 1341 Cov.: 33 AF XY: 0.127 AC XY: 9481 AN XY: 74448

African (AFR) AF: 0.161 AC: 6696 AN: 41528

American (AMR) AF: 0.129 AC: 1971 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0766 AC: 266 AN: 3472

East Asian (EAS) AF: 0.226 AC: 1169 AN: 5184

South Asian (SAS) AF: 0.223 AC: 1077 AN: 4824

European-Finnish (FIN) AF: 0.115 AC: 1224 AN: 10604

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0855 AC: 5817 AN: 68020

Other (OTH) AF: 0.122 AC: 258 AN: 2112

Alfa AF: 0.109 Hom.: 358

Bravo AF: 0.123

Asia WGS AF: 0.227 AC: 788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	15
DANN	Benign	0.86
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs4421324; hg19: chr8-95124056;