rs12208390

Variant names:

• chr6-26436878-C-T
• rs12208390
• ENST00000707189.1:n.1000-116309C>T

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.1000-116309C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0736 in 152,214 control chromosomes in the GnomAD database, including 651 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 0.074 (651 hom., cov: 32)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 14 publications found

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.094 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
ENSG00000291336	ENST00000707189.1	n.1000-116309C>T		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1001-95827C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0738 AC: 11219 AN: 152096 Hom.: 653 Cov.: 32

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0608

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0750

Gnomad SAS AF: 0.0217

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0960

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0736 AC: 11208 AN: 152214 Hom.: 651 Cov.: 32 AF XY: 0.0777 AC XY: 5779 AN XY: 74408

African (AFR) AF: 0.0162 AC: 673 AN: 41554

American (AMR) AF: 0.0606 AC: 927 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3470

East Asian (EAS) AF: 0.0744 AC: 385 AN: 5176

South Asian (SAS) AF: 0.0215 AC: 104 AN: 4828

European-Finnish (FIN) AF: 0.216 AC: 2289 AN: 10582

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0960 AC: 6525 AN: 67992

Other (OTH) AF: 0.0525 AC: 111 AN: 2114

Alfa AF: 0.0814 Hom.: 994

Bravo AF: 0.0605

Asia WGS AF: 0.0310 AC: 110 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs12208390; hg19: chr6-26437106;