chr6-26354552-A-C

Variant names:

• chr6-26354552-A-C
• rs9379851
• ENST00000707189.1:n.1000-198635A>C

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.1000-198635A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0769 in 152,256 control chromosomes in the GnomAD database, including 567 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 0.077 (567 hom., cov: 32)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 32 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000707189.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291336	ENST00000707189.1		n.1000-198635A>C		intron	N/A
	ENSG00000291338	ENST00000707191.1		n.1001-178153A>C		intron	N/A
	ENSG00000300412	ENST00000771472.1		n.160-995A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0770 AC: 11718 AN: 152138 Hom.: 568 Cov.: 32

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0864

Gnomad SAS AF: 0.0983

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0701

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

GnomAD4 genome AF: 0.0769 AC: 11709 AN: 152256 Hom.: 567 Cov.: 32 AF XY: 0.0737 AC XY: 5489 AN XY: 74440

African (AFR) AF: 0.0344 AC: 1429 AN: 41550

American (AMR) AF: 0.0408 AC: 624 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3470

East Asian (EAS) AF: 0.0866 AC: 448 AN: 5174

South Asian (SAS) AF: 0.0972 AC: 469 AN: 4826

European-Finnish (FIN) AF: 0.0713 AC: 757 AN: 10616

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7543 AN: 68006

Other (OTH) AF: 0.0703 AC: 148 AN: 2106

Alfa AF: 0.103 Hom.: 1721

Bravo AF: 0.0721

Asia WGS AF: 0.0990 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.75
DANN	Benign	0.40
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs9379851; hg19: chr6-26354780;