rs7103004

Positions:

• chr11-103655296-C-T

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 0.487 in 151,876 control chromosomes in the GnomAD database, including 19,726 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 0.49 (19726 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.103655296C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73900 AN: 151760 Hom.: 19719 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.482

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

GnomAD4 genome AF: 0.487 AC: 73927 AN: 151876 Hom.: 19726 Cov.: 32 AF XY: 0.487 AC XY: 36127 AN XY: 74234

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.487

Alfa AF: 0.545 Hom.: 3743

Bravo AF: 0.469

Asia WGS AF: 0.501 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.91
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7103004; hg19: chr11-103526024;