rs7109663

Positions:

• chr11-102641030-G-C
• chr11-102641030-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 11-102641030-G-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,056 control chromosomes in the GnomAD database, including 9,187 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 0.34 (9187 hom., cov: 32)
• Consequence: ENST00000702066.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.389 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
	ENST00000702066.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51985 AN: 151938 Hom.: 9180 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.342 AC: 52008 AN: 152056 Hom.: 9187 Cov.: 32 AF XY: 0.345 AC XY: 25651 AN XY: 74334

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.425

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.350

Alfa AF: 0.360 Hom.: 1257

Bravo AF: 0.333

Asia WGS AF: 0.356 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7109663; hg19: chr11-102511761;