7-116656842-C-T

Position:

• chr7-116656842-C-T

Variant summary

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

The NR_165032.1(COMETT):​n.390+6897G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,982 control chromosomes in the GnomAD database, including 28,904 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 0.58 (28904 hom., cov: 33)
• Consequence: COMETT NR_165032.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237

Genes affected

COMETT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COMETT	NR_165032.1	n.390+6897G>A		intron_variant
COMETT	NR_165033.1	n.390+6897G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COMETT	ENST00000650435.1	n.92-1178G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88493 AN: 151864 Hom.: 28907 Cov.: 33

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.704

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.582 AC: 88503 AN: 151982 Hom.: 28904 Cov.: 33 AF XY: 0.588 AC XY: 43703 AN XY: 74318

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.690

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.704

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.616

Alfa AF: 0.693 Hom.: 49602

Bravo AF: 0.571

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.4
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs437; hg19: chr7-116296896; COSMIC: COSV70617798;