12-62983598-C-T

Variant names:

• chr12-62983598-C-T
• rs699615
• ENST00000826462.1:n.119+16159C>T

Variant summary

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

The ENST00000826462.1(ENSG00000307468):​n.119+16159C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.918 in 152,268 control chromosomes in the GnomAD database, including 64,251 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 0.92 (64251 hom., cov: 32)
• Consequence: ENSG00000307468 ENST00000826462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363
• Publications: 1 publications found

Genes affected

ENSG00000307468 (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 (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826462.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307468	ENST00000826462.1		n.119+16159C>T		intron	N/A
	ENSG00000307468	ENST00000826463.1		n.183+13163C>T		intron	N/A
	ENSG00000307468	ENST00000826464.1		n.131+5866C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.918 AC: 139723 AN: 152150 Hom.: 64201 Cov.: 32

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.918 AC: 139832 AN: 152268 Hom.: 64251 Cov.: 32 AF XY: 0.919 AC XY: 68372 AN XY: 74438

African (AFR) AF: 0.909 AC: 37766 AN: 41552

American (AMR) AF: 0.931 AC: 14242 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3192 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5155 AN: 5176

South Asian (SAS) AF: 0.943 AC: 4545 AN: 4820

European-Finnish (FIN) AF: 0.921 AC: 9777 AN: 10612

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.913 AC: 62076 AN: 68016

Other (OTH) AF: 0.917 AC: 1938 AN: 2114

Alfa AF: 0.914 Hom.: 77887

Bravo AF: 0.918

Asia WGS AF: 0.963 AC: 3351 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	1.3
DANN	Benign	0.16
PhyloP100		-0.36

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs699615;

hg19: chr12-63377378;