rs6926835

Variant names:

• chr6-12227312-A-C
• rs6926835
• ENST00000789282.1:n.115+27692T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-12227312-A-C
• chr6-12227312-A-T

Variant summary

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

The ENST00000789282.1(ENSG00000302734):​n.115+27692T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,182 control chromosomes in the GnomAD database, including 5,008 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 0.24 (5008 hom., cov: 32)
• Consequence: ENSG00000302734 ENST00000789282.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.831
• Publications: 1 publications found

Genes affected

ENSG00000302734 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.312 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
ENSG00000302734	ENST00000789282.1	n.115+27692T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36402 AN: 152064 Hom.: 5003 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.239 AC: 36422 AN: 152182 Hom.: 5008 Cov.: 32 AF XY: 0.237 AC XY: 17659 AN XY: 74400

African (AFR) AF: 0.104 AC: 4317 AN: 41532

American (AMR) AF: 0.275 AC: 4198 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 901 AN: 3468

East Asian (EAS) AF: 0.224 AC: 1162 AN: 5182

South Asian (SAS) AF: 0.137 AC: 662 AN: 4826

European-Finnish (FIN) AF: 0.282 AC: 2982 AN: 10580

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21445 AN: 67986

Other (OTH) AF: 0.266 AC: 563 AN: 2114

Alfa AF: 0.261 Hom.: 2578

Bravo AF: 0.236

Asia WGS AF: 0.195 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.2
DANN	Benign	0.37
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs6926835; hg19: chr6-12227545;