chr11-6664327-G-A

Variant names:

• chr11-6664327-G-A
• rs10500664
• ENST00000811755.1:n.*109G>A

Variant summary

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

The ENST00000811755.1(ENSG00000255410):​n.*109G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,040 control chromosomes in the GnomAD database, including 55,694 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 0.85 (55694 hom., cov: 30)
• Consequence: ENSG00000255410 ENST00000811755.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180
• Publications: 7 publications found

Genes affected

ENSG00000255410 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000811755.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000255410	ENST00000811755.1		n.*109G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.849 AC: 129046 AN: 151924 Hom.: 55652 Cov.: 30

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.849 AC: 129145 AN: 152040 Hom.: 55694 Cov.: 30 AF XY: 0.852 AC XY: 63329 AN XY: 74344

African (AFR) AF: 0.687 AC: 28416 AN: 41372

American (AMR) AF: 0.909 AC: 13894 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3169 AN: 3470

East Asian (EAS) AF: 0.987 AC: 5116 AN: 5186

South Asian (SAS) AF: 0.781 AC: 3757 AN: 4808

European-Finnish (FIN) AF: 0.949 AC: 10054 AN: 10592

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.908 AC: 61783 AN: 68008

Other (OTH) AF: 0.872 AC: 1841 AN: 2112

Alfa AF: 0.884 Hom.: 110698

Bravo AF: 0.841

Asia WGS AF: 0.847 AC: 2946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
DANN	Benign	0.57
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10500664; hg19: chr11-6685558;