chr11-34680611-G-T

Variant names:

• chr11-34680611-G-T
• rs286873

Variant summary

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

The variant allele was found at a frequency of 0.111 in 152,072 control chromosomes in the GnomAD database, including 1,106 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 0.11 (1106 hom., cov: 32)
• Consequence: NDUFB8P3 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.406
• Publications: 5 publications found

Genes affected

NDUFB8P3 (HGNC:33979):

ENSG00000309708 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDUFB8P3		n.34680611G>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309708	ENST00000843229.1	n.488+4628C>A		intron_variant	Intron 2 of 5
ENSG00000309708	ENST00000843230.1	n.532+4628C>A		intron_variant	Intron 2 of 3
ENSG00000309708	ENST00000843231.1	n.280+4628C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16837 AN: 151954 Hom.: 1108 Cov.: 32

Gnomad AFR AF: 0.0825

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0896

Gnomad ASJ AF: 0.0643

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.111 AC: 16842 AN: 152072 Hom.: 1106 Cov.: 32 AF XY: 0.119 AC XY: 8831 AN XY: 74302

African (AFR) AF: 0.0825 AC: 3423 AN: 41508

American (AMR) AF: 0.0902 AC: 1377 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0643 AC: 223 AN: 3470

East Asian (EAS) AF: 0.304 AC: 1569 AN: 5162

South Asian (SAS) AF: 0.254 AC: 1223 AN: 4818

European-Finnish (FIN) AF: 0.191 AC: 2016 AN: 10566

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0990 AC: 6725 AN: 67958

Other (OTH) AF: 0.0927 AC: 196 AN: 2114

Alfa AF: 0.0997 Hom.: 3415

Bravo AF: 0.0992

Asia WGS AF: 0.277 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.8
DANN	Benign	0.58
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs286873; hg19: chr11-34702158;