rs12208390

Positions:

• chr6-26436878-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000707189.1(ENSG00000291336):​n.1000-116309C>T variant causes a intron, non coding transcript 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: ENST00000707189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000707189.1	n.1000-116309C>T		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-95827C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0162

Gnomad4 AMR AF: 0.0606

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.0744

Gnomad4 SAS AF: 0.0215

Gnomad4 FIN AF: 0.216

Gnomad4 NFE AF: 0.0960

Gnomad4 OTH AF: 0.0525

Alfa AF: 0.0850 Hom.: 737

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12208390; hg19: chr6-26437106;