rs3021529

Variant names:

• chr12-63151900-G-A
• rs3021529
• ENST00000789607.1:n.337C>T

Variant summary

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

The ENST00000789607.1(ENSG00000302797):​n.337C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,132 control chromosomes in the GnomAD database, including 1,301 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 0.13 (1301 hom., cov: 32)
• Consequence: ENSG00000302797 ENST00000789607.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.206
• Publications: 16 publications found

Genes affected

ENSG00000302797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000789607.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302797	ENST00000789607.1		n.337C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000279444	ENST00000624438.1	TSL:5	n.29-581G>A		intron	N/A
	ENSG00000302777	ENST00000789492.1		n.340-581G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19215 AN: 152014 Hom.: 1299 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0380

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.126 AC: 19235 AN: 152132 Hom.: 1301 Cov.: 32 AF XY: 0.125 AC XY: 9274 AN XY: 74362

African (AFR) AF: 0.112 AC: 4654 AN: 41510

American (AMR) AF: 0.110 AC: 1682 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 539 AN: 3472

East Asian (EAS) AF: 0.0383 AC: 198 AN: 5168

South Asian (SAS) AF: 0.160 AC: 770 AN: 4808

European-Finnish (FIN) AF: 0.0944 AC: 999 AN: 10588

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9869 AN: 67982

Other (OTH) AF: 0.121 AC: 255 AN: 2108

Alfa AF: 0.138 Hom.: 2449

Bravo AF: 0.123

Asia WGS AF: 0.0980 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.1
DANN	Benign	0.93
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs3021529; hg19: chr12-63545680;