rs12151565

Positions:

• chr2-22275718-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000450551.1(ENSG00000228999):​n.71-64724C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0679 in 152,178 control chromosomes in the GnomAD database, including 606 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 0.068 (606 hom., cov: 31)
• Consequence: ENST00000450551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000450551.1	n.71-64724C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0678 AC: 10317 AN: 152060 Hom.: 600 Cov.: 31

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.0115

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0679

Gnomad FIN AF: 0.0291

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0191

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0679 AC: 10336 AN: 152178 Hom.: 606 Cov.: 31 AF XY: 0.0683 AC XY: 5085 AN XY: 74420

Gnomad4 AFR AF: 0.148

Gnomad4 AMR AF: 0.0976

Gnomad4 ASJ AF: 0.0115

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.0678

Gnomad4 FIN AF: 0.0291

Gnomad4 NFE AF: 0.0191

Gnomad4 OTH AF: 0.0663

Alfa AF: 0.0604 Hom.: 84

Bravo AF: 0.0778

Asia WGS AF: 0.0900 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.2
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12151565; hg19: chr2-22498590;