rs7959363

Variant names:

• chr12-124624381-A-G
• rs7959363
• ENST00000767262.1:n.309-18022T>C

Variant summary

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

The ENST00000767262.1(ENSG00000299894):​n.309-18022T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0866 in 152,246 control chromosomes in the GnomAD database, including 676 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 0.087 (676 hom., cov: 33)
• Consequence: ENSG00000299894 ENST00000767262.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344
• Publications: 4 publications found

Genes affected

ENSG00000299894 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000767262.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299894	ENST00000767262.1		n.309-18022T>C		intron	N/A
	ENSG00000299911	ENST00000767386.1		n.333-2843T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0866 AC: 13172 AN: 152128 Hom.: 677 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0512

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.0696

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.0585

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0695

Gnomad OTH AF: 0.0742

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

GnomAD4 genome AF: 0.0866 AC: 13189 AN: 152246 Hom.: 676 Cov.: 33 AF XY: 0.0843 AC XY: 6277 AN XY: 74448

African (AFR) AF: 0.144 AC: 5968 AN: 41528

American (AMR) AF: 0.0511 AC: 782 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3470

East Asian (EAS) AF: 0.0694 AC: 360 AN: 5188

South Asian (SAS) AF: 0.0739 AC: 357 AN: 4832

European-Finnish (FIN) AF: 0.0585 AC: 620 AN: 10598

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0695 AC: 4727 AN: 68014

Other (OTH) AF: 0.0791 AC: 167 AN: 2112

Alfa AF: 0.0764 Hom.: 774

Bravo AF: 0.0877

Asia WGS AF: 0.0700 AC: 244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.83
DANN	Benign	0.43
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs7959363; hg19: chr12-125108927;