chr12-53771229-T-C

Variant names:

• chr12-53771229-T-C
• rs11170681
• ENST00000652339.1:n.213+31341T>C

Variant summary

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

The NR_189097.1(LOC105378250):​n.295+31341T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,084 control chromosomes in the GnomAD database, including 3,763 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 0.21 (3763 hom., cov: 32)
• Consequence: LOC105378250 NR_189097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188
• Publications: 8 publications found

Genes affected

ENSG00000286069 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_189097.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105378250	NR_189097.1		n.295+31341T>C		intron	N/A
	LOC105378250	NR_189098.1		n.295+31341T>C		intron	N/A
	LOC105378250	NR_189099.1		n.295+31341T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286069	ENST00000652339.1		n.213+31341T>C		intron	N/A
	ENSG00000286069	ENST00000654713.2		n.214+31341T>C		intron	N/A
	ENSG00000286069	ENST00000656247.1		n.143+20239T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32118 AN: 151964 Hom.: 3757 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.0705

Gnomad SAS AF: 0.0995

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.211 AC: 32145 AN: 152084 Hom.: 3763 Cov.: 32 AF XY: 0.205 AC XY: 15207 AN XY: 74348

African (AFR) AF: 0.299 AC: 12398 AN: 41456

American (AMR) AF: 0.199 AC: 3037 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 613 AN: 3470

East Asian (EAS) AF: 0.0707 AC: 366 AN: 5176

South Asian (SAS) AF: 0.0995 AC: 479 AN: 4812

European-Finnish (FIN) AF: 0.102 AC: 1078 AN: 10592

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13435 AN: 67988

Other (OTH) AF: 0.202 AC: 426 AN: 2114

Alfa AF: 0.205 Hom.: 10941

Bravo AF: 0.224

Asia WGS AF: 0.111 AC: 386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.9
DANN	Benign	0.52
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs11170681; hg19: chr12-54165013;