chr12-41609068-G-A

Variant names:

• chr12-41609068-G-A
• rs286980
• ENST00000779513.1:n.96-2896C>T

Variant summary

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

The ENST00000779513.1(ENSG00000301531):​n.96-2896C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,840 control chromosomes in the GnomAD database, including 16,037 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 0.46 (16037 hom., cov: 32)
• Consequence: ENSG00000301531 ENST00000779513.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 4 publications found

Genes affected

ENSG00000301531 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000779513.1. 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
	ENSG00000301531	ENST00000779513.1		n.96-2896C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69371 AN: 151722 Hom.: 16035 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.457 AC: 69399 AN: 151840 Hom.: 16037 Cov.: 32 AF XY: 0.459 AC XY: 34040 AN XY: 74200

African (AFR) AF: 0.432 AC: 17888 AN: 41424

American (AMR) AF: 0.485 AC: 7385 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1532 AN: 3472

East Asian (EAS) AF: 0.572 AC: 2950 AN: 5158

South Asian (SAS) AF: 0.541 AC: 2601 AN: 4810

European-Finnish (FIN) AF: 0.393 AC: 4139 AN: 10540

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.464 AC: 31480 AN: 67902

Other (OTH) AF: 0.461 AC: 972 AN: 2110

Alfa AF: 0.460 Hom.: 2638

Bravo AF: 0.459

Asia WGS AF: 0.508 AC: 1753 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.78
DANN	Benign	0.74
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs286980; hg19: chr12-42002870;