6-26200449-A-G

Variant names:

• chr6-26200449-A-G
• rs806794
• ENST00000707189.1:n.999+76278A>G

Variant summary

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

The ENST00000707189.1(ENSG00000291336):​n.999+76278A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000291336 ENST00000707189.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.606
• Publications: 84 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291336	ENST00000707189.1		n.999+76278A>G		intron	N/A
	ENSG00000291338	ENST00000707191.1		n.1000+42328A>G		intron	N/A
	ENSG00000301014	ENST00000775520.1		n.135-1969A>G		intron	N/A

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

African (AFR) AF: 0.333 AC: 20 AN: 60

American (AMR) AF: 0.449 AC: 497 AN: 1108

Ashkenazi Jewish (ASJ) AF: 0.392 AC: 40 AN: 102

East Asian (EAS) AF: 0.810 AC: 136 AN: 168

South Asian (SAS) AF: 0.422 AC: 343 AN: 812

European-Finnish (FIN) AF: 0.348 AC: 55 AN: 158

Middle Eastern (MID) AF: 0.333 AC: 6 AN: 18

European-Non Finnish (NFE) AF: 0.285 AC: 1185 AN: 4164

Other (OTH) AF: 0.374 AC: 127 AN: 340

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

African (AFR) AF: 0.378 AC: 15667 AN: 41490

American (AMR) AF: 0.395 AC: 6040 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1616 AN: 3470

East Asian (EAS) AF: 0.755 AC: 3918 AN: 5192

South Asian (SAS) AF: 0.429 AC: 2067 AN: 4822

European-Finnish (FIN) AF: 0.442 AC: 4669 AN: 10558

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19957 AN: 67986

Other (OTH) AF: 0.364 AC: 770 AN: 2114

Alfa AF: 0.329 Hom.: 29063

Bravo AF: 0.359

Asia WGS AF: 0.549 AC: 1909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.47
PhyloP100		0.61
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

Other links and lift over

dbSNP: rs806794; hg19: chr6-26200677;