chr11-107681196-C-A

Position:

• chr11-107681196-C-A

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 0.771 in 152,148 control chromosomes in the GnomAD database, including 45,863 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 0.77 (45863 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.785

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.107681196C>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117179 AN: 152030 Hom.: 45810 Cov.: 32

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.771 AC: 117290 AN: 152148 Hom.: 45863 Cov.: 32 AF XY: 0.773 AC XY: 57473 AN XY: 74386

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.704

Gnomad4 OTH AF: 0.765

Alfa AF: 0.720 Hom.: 19376

Bravo AF: 0.786

Asia WGS AF: 0.748 AC: 2602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.43
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1790137; hg19: chr11-107551922;