chr12-121607669-T-C

Variant names:

• chr12-121607669-T-C
• rs7962930
• ENST00000786201.1:n.180-11634A>G

Variant summary

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

The ENST00000786201.1(ENSG00000302371):​n.180-11634A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,934 control chromosomes in the GnomAD database, including 4,457 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 0.23 (4457 hom., cov: 32)
• Consequence: ENSG00000302371 ENST00000786201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 5 publications found

Genes affected

ENSG00000302371 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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
ENSG00000302371	ENST00000786201.1	n.180-11634A>G		intron_variant	Intron 1 of 2
ENSG00000302371	ENST00000786202.1	n.182-11634A>G		intron_variant	Intron 1 of 3
ENSG00000302371	ENST00000786203.1	n.180-11634A>G		intron_variant	Intron 1 of 2
ENSG00000302371	ENST00000786204.1	n.55-11634A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35578 AN: 151816 Hom.: 4451 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0974

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.234 AC: 35605 AN: 151934 Hom.: 4457 Cov.: 32 AF XY: 0.231 AC XY: 17178 AN XY: 74274

African (AFR) AF: 0.294 AC: 12161 AN: 41412

American (AMR) AF: 0.162 AC: 2470 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3468

East Asian (EAS) AF: 0.0976 AC: 504 AN: 5164

South Asian (SAS) AF: 0.114 AC: 548 AN: 4810

European-Finnish (FIN) AF: 0.274 AC: 2886 AN: 10538

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15927 AN: 67970

Other (OTH) AF: 0.197 AC: 416 AN: 2112

Alfa AF: 0.225 Hom.: 12631

Bravo AF: 0.229

Asia WGS AF: 0.100 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.8
DANN	Benign	0.91
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs7962930; hg19: chr12-122045574;