12-49063852-G-A

Variant names:

• chr12-49063852-G-A
• rs11168839
• ENST00000780157.1:n.*18G>A

Variant summary

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

The ENST00000780157.1(ENSG00000301605):​n.*18G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,068 control chromosomes in the GnomAD database, including 12,802 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 0.41 (12802 hom., cov: 32)
• Consequence: ENSG00000301605 ENST00000780157.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 15 publications found

Genes affected

ENSG00000301605 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780157.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301605	ENST00000780157.1		n.*18G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61685 AN: 151950 Hom.: 12775 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.406 AC: 61762 AN: 152068 Hom.: 12802 Cov.: 32 AF XY: 0.405 AC XY: 30102 AN XY: 74320

African (AFR) AF: 0.476 AC: 19744 AN: 41462

American (AMR) AF: 0.335 AC: 5117 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3472

East Asian (EAS) AF: 0.416 AC: 2153 AN: 5180

South Asian (SAS) AF: 0.468 AC: 2257 AN: 4826

European-Finnish (FIN) AF: 0.413 AC: 4363 AN: 10558

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.384 AC: 26074 AN: 67980

Other (OTH) AF: 0.372 AC: 786 AN: 2114

Alfa AF: 0.383 Hom.: 34450

Bravo AF: 0.396

Asia WGS AF: 0.437 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.3
DANN	Benign	0.68
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs11168839; hg19: chr12-49457635;