6-26455277-G-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000291336 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.685

Gnomad4 ASJ AF: 0.696

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.657

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6456723; hg19: chr6-26455505;