rs12150211

Variant names:

• chr17-27807406-G-A
• rs12150211
• ENST00000582441.1:c.220-3065C>T

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-3065C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.273 in 150,142 control chromosomes in the GnomAD database, including 5,829 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 0.27 (5829 hom., cov: 30)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 6 publications found

Genes affected

ENSG00000266202 (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 (AMR) allele frequency at 95% confidence interval = 0.35 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
ENSG00000266202	ENST00000582441.1	c.220-3065C>T		intron_variant	Intron 3 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41007 AN: 150056 Hom.: 5825 Cov.: 30

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.273 AC: 41037 AN: 150142 Hom.: 5829 Cov.: 30 AF XY: 0.278 AC XY: 20361 AN XY: 73186

African (AFR) AF: 0.211 AC: 8607 AN: 40886

American (AMR) AF: 0.358 AC: 5422 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 937 AN: 3462

East Asian (EAS) AF: 0.263 AC: 1349 AN: 5120

South Asian (SAS) AF: 0.351 AC: 1670 AN: 4762

European-Finnish (FIN) AF: 0.317 AC: 3101 AN: 9788

Middle Eastern (MID) AF: 0.203 AC: 59 AN: 290

European-Non Finnish (NFE) AF: 0.281 AC: 19054 AN: 67698

Other (OTH) AF: 0.264 AC: 551 AN: 2084

Alfa AF: 0.268 Hom.: 783

Bravo AF: 0.271

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.73
DANN	Benign	0.26
PhyloP100		-0.12

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs12150211; hg19: chr17-26134432;