chr12-38349706-G-A

Variant names:

• chr12-38349706-G-A
• rs6582630
• ENST00000783312.1:n.230-4843G>A

Variant summary

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

The ENST00000783312.1(ENSG00000302012):​n.230-4843G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 151,820 control chromosomes in the GnomAD database, including 29,989 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 0.62 (29989 hom., cov: 31)
• Consequence: ENSG00000302012 ENST00000783312.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 20 publications found

Genes affected

ENSG00000302012 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 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
ENSG00000302012	ENST00000783312.1	n.230-4843G>A		intron_variant	Intron 1 of 2
ENSG00000302012	ENST00000783313.1	n.329-4843G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93966 AN: 151702 Hom.: 29940 Cov.: 31

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.620 AC: 94074 AN: 151820 Hom.: 29989 Cov.: 31 AF XY: 0.624 AC XY: 46315 AN XY: 74194

African (AFR) AF: 0.728 AC: 30164 AN: 41424

American (AMR) AF: 0.660 AC: 10052 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1825 AN: 3462

East Asian (EAS) AF: 0.843 AC: 4341 AN: 5152

South Asian (SAS) AF: 0.693 AC: 3338 AN: 4820

European-Finnish (FIN) AF: 0.592 AC: 6243 AN: 10552

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36279 AN: 67870

Other (OTH) AF: 0.573 AC: 1206 AN: 2106

Alfa AF: 0.567 Hom.: 35444

Bravo AF: 0.632

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.63
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs6582630; hg19: chr12-38743508;