3-124013864-G-C

Variant names:

• chr3-124013864-G-C
• rs9813249
• ENST00000801819.1:n.81-18395G>C

Variant summary

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

The ENST00000801819.1(ENSG00000304291):​n.81-18395G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,152 control chromosomes in the GnomAD database, including 1,582 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 (1582 hom., cov: 32)
• Consequence: ENSG00000304291 ENST00000801819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.544
• Publications: 0 publications found

Genes affected

ENSG00000304291 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000801819.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304291	ENST00000801819.1		n.81-18395G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17611 AN: 152034 Hom.: 1573 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.0631

Gnomad EAS AF: 0.00753

Gnomad SAS AF: 0.0232

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.116 AC: 17652 AN: 152152 Hom.: 1582 Cov.: 32 AF XY: 0.113 AC XY: 8382 AN XY: 74388

African (AFR) AF: 0.246 AC: 10203 AN: 41490

American (AMR) AF: 0.0827 AC: 1266 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0631 AC: 219 AN: 3470

East Asian (EAS) AF: 0.00755 AC: 39 AN: 5168

South Asian (SAS) AF: 0.0230 AC: 111 AN: 4816

European-Finnish (FIN) AF: 0.0713 AC: 756 AN: 10606

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0680 AC: 4621 AN: 67990

Other (OTH) AF: 0.121 AC: 255 AN: 2106

Alfa AF: 0.0853 Hom.: 106

Bravo AF: 0.124

Asia WGS AF: 0.0390 AC: 134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.48
PhyloP100		0.54

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9813249;

hg19: chr3-123732711;