6-26200449-A-G

Position:

• chr6-26200449-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.362 in 159,044 control chromosomes in the GnomAD database, including 11,153 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 0.36 (10630 hom., cov: 32)
  • Exomes 𝑓: 0.35 (523 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.26200449A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291336	ENST00000707189.1	n.999+76278A>G		intron_variant
ENSG00000291338	ENST00000707191.1	n.1000+42328A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55069 AN: 151996 Hom.: 10603 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.362

GnomAD4 exome AF: 0.348 AC: 2409 AN: 6930 Hom.: 523 Cov.: 0 AF XY: 0.349 AC XY: 1286 AN XY: 3688

Gnomad4 AFR exome AF: 0.333

Gnomad4 AMR exome AF: 0.449

Gnomad4 ASJ exome AF: 0.392

Gnomad4 EAS exome AF: 0.810

Gnomad4 SAS exome AF: 0.422

Gnomad4 FIN exome AF: 0.348

Gnomad4 NFE exome AF: 0.285

Gnomad4 OTH exome AF: 0.374

GnomAD4 genome AF: 0.363 AC: 55156 AN: 152114 Hom.: 10630 Cov.: 32 AF XY: 0.374 AC XY: 27823 AN XY: 74344

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.364

Alfa AF: 0.325 Hom.: 11462

Bravo AF: 0.359

Asia WGS AF: 0.549 AC: 1909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.47
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs806794; hg19: chr6-26200677;