rs7109806

Variant names:

• chr11-8221082-T-C
• rs7109806
• ENST00000825479.1:n.229-2622T>C

Variant summary

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

The ENST00000825479.1(ENSG00000307368):​n.229-2622T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,040 control chromosomes in the GnomAD database, including 3,124 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 0.16 (3124 hom., cov: 33)
• Consequence: ENSG00000307368 ENST00000825479.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695
• Publications: 5 publications found

Genes affected

ENSG00000307368 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825479.1. 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
	ENSG00000307368	ENST00000825479.1		n.229-2622T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24253 AN: 151922 Hom.: 3117 Cov.: 33

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.0568

Gnomad SAS AF: 0.0479

Gnomad FIN AF: 0.0990

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.160 AC: 24292 AN: 152040 Hom.: 3124 Cov.: 33 AF XY: 0.157 AC XY: 11683 AN XY: 74328

African (AFR) AF: 0.353 AC: 14634 AN: 41450

American (AMR) AF: 0.104 AC: 1593 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3470

East Asian (EAS) AF: 0.0573 AC: 295 AN: 5148

South Asian (SAS) AF: 0.0473 AC: 228 AN: 4822

European-Finnish (FIN) AF: 0.0990 AC: 1047 AN: 10572

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0849 AC: 5772 AN: 67982

Other (OTH) AF: 0.131 AC: 276 AN: 2112

Alfa AF: 0.106 Hom.: 1636

Bravo AF: 0.171

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs7109806; hg19: chr11-8242629;