12-47571501-G-A

Variant names:

• chr12-47571501-G-A
• rs1234818
• ENST00000799111.1:n.90+16971G>A

Variant summary

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

The ENST00000799111.1(ENSG00000304045):​n.90+16971G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,944 control chromosomes in the GnomAD database, including 17,912 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 0.48 (17912 hom., cov: 32)
• Consequence: ENSG00000304045 ENST00000799111.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 4 publications found

Genes affected

ENSG00000304045 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000799111.1. 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
	ENSG00000304045	ENST00000799111.1		n.90+16971G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73194 AN: 151826 Hom.: 17889 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.482 AC: 73263 AN: 151944 Hom.: 17912 Cov.: 32 AF XY: 0.487 AC XY: 36141 AN XY: 74254

African (AFR) AF: 0.476 AC: 19719 AN: 41430

American (AMR) AF: 0.615 AC: 9388 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1848 AN: 3466

East Asian (EAS) AF: 0.421 AC: 2178 AN: 5178

South Asian (SAS) AF: 0.477 AC: 2298 AN: 4822

European-Finnish (FIN) AF: 0.518 AC: 5453 AN: 10534

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30799 AN: 67952

Other (OTH) AF: 0.512 AC: 1077 AN: 2104

Alfa AF: 0.464 Hom.: 8483

Bravo AF: 0.492

Asia WGS AF: 0.532 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	5.9
DANN	Benign	0.64
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1234818; hg19: chr12-47965284;