rs184953

Positions:

• chr7-116671876-A-C
• chr7-116671876-A-G
• chr7-116671876-A-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 0.861 in 152,156 control chromosomes in the GnomAD database, including 56,484 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 0.86 (56484 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.861

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.116671876A>C		intergenic_region
COMETT	NR_165032.1	n.88-7835T>G		intron_variant
COMETT	NR_165033.1	n.88-7835T>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.861 AC: 130898 AN: 152038 Hom.: 56438 Cov.: 32

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.887

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.879

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.857

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

GnomAD4 genome AF: 0.861 AC: 131002 AN: 152156 Hom.: 56484 Cov.: 32 AF XY: 0.864 AC XY: 64278 AN XY: 74370

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.887

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.843

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.855

Alfa AF: 0.833 Hom.: 14151

Bravo AF: 0.865

Asia WGS AF: 0.848 AC: 2949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.0
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: rs184953; hg19: chr7-116311930;