rs12206812

Variant names:

• chr6-26436364-C-T
• rs12206812
• ENST00000707189.1:n.1000-116823C>T

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.1000-116823C>T variant causes a intron 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: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 6 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=-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000291336	ENST00000707189.1	n.1000-116823C>T		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1001-96341C>T		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.176 AC: 7284 AN: 41340

American (AMR) AF: 0.181 AC: 2752 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 692 AN: 3464

East Asian (EAS) AF: 0.0330 AC: 170 AN: 5154

South Asian (SAS) AF: 0.217 AC: 1042 AN: 4804

European-Finnish (FIN) AF: 0.172 AC: 1808 AN: 10532

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11333 AN: 67846

Other (OTH) AF: 0.157 AC: 331 AN: 2112

Alfa AF: 0.168 Hom.: 1385

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs12206812; hg19: chr6-26436592;