rs12206812

Positions:

• chr6-26436364-C-T

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.1000-116823C>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 0.169 in 151,700 control chromosomes in the GnomAD database, including 2,252 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 0.17 (2252 hom., cov: 30)
• Consequence: ENST00000707189.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000707189.1	n.1000-116823C>T		intron_variant, non_coding_transcript_variant
	ENST00000707191.1	n.1001-96341C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25641 AN: 151582 Hom.: 2248 Cov.: 30

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.0325

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.169 AC: 25671 AN: 151700 Hom.: 2252 Cov.: 30 AF XY: 0.170 AC XY: 12590 AN XY: 74126

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.200

Gnomad4 EAS AF: 0.0330

Gnomad4 SAS AF: 0.217

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.157

Alfa AF: 0.171 Hom.: 887

Bravo AF: 0.169

Asia WGS AF: 0.115 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12206812; hg19: chr6-26436592;