rs7109806

Positions:

• chr11-8221082-T-C

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 0.16 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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.0790

Gnomad4 EAS AF: 0.0573

Gnomad4 SAS AF: 0.0473

Gnomad4 FIN AF: 0.0990

Gnomad4 NFE AF: 0.0849

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0940 Hom.: 914

Bravo AF: 0.171

Asia WGS AF: 0.101 AC: 351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7109806; hg19: chr11-8242629;