chr6-26455277-G-C

Variant names:

• chr6-26455277-G-C
• rs6456723
• ENST00000707189.1:n.1000-97910G>C

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.1000-97910G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,088 control chromosomes in the GnomAD database, including 35,323 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 0.65 (35323 hom., cov: 32)
• Consequence: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 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.1000-97910G>C		intron_variant	Intron 1 of 1
ENSG00000291338	ENST00000707191.1	n.1001-77428G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98791 AN: 151970 Hom.: 35319 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.650 AC: 98816 AN: 152088 Hom.: 35323 Cov.: 32 AF XY: 0.652 AC XY: 48511 AN XY: 74362

African (AFR) AF: 0.330 AC: 13688 AN: 41450

American (AMR) AF: 0.685 AC: 10467 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2416 AN: 3472

East Asian (EAS) AF: 0.820 AC: 4250 AN: 5184

South Asian (SAS) AF: 0.681 AC: 3282 AN: 4822

European-Finnish (FIN) AF: 0.802 AC: 8502 AN: 10600

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53936 AN: 67978

Other (OTH) AF: 0.657 AC: 1380 AN: 2102

Alfa AF: 0.714 Hom.: 5130

Bravo AF: 0.624

Asia WGS AF: 0.736 AC: 2563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.32
DANN	Benign	0.33
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs6456723; hg19: chr6-26455505;