chr6-142301906-T-C

Position:

• chr6-142301906-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000367608.6(ADGRG6):​c.-424T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0548 in 213,810 control chromosomes in the GnomAD database, including 1,385 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.073 (1316 hom., cov: 32)
  • Exomes 𝑓: 0.012 (69 hom.)
• Consequence: ADGRG6 ENST00000367608.6 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0620

Genes affected

ADGRG6 (HGNC:13841): (adhesion G protein-coupled receptor G6) This gene, which is upregulated in human umbilical vein endothelial cells, encodes a G protein-coupled receptor. Variations in this gene can affect a person's stature. Multiple transcript variants encoding different proteins have been found for this gene. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 6-142301906-T-C is Benign according to our data. Variant chr6-142301906-T-C is described in ClinVar as [Benign]. Clinvar id is 1295007.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADGRG6	ENST00000230173.10	c.-424T>C		5_prime_UTR_variant	1/26	1
ADGRG6	ENST00000367608.6	c.-424T>C		5_prime_UTR_variant	1/24	1		P1
ADGRG6	ENST00000415128.6			upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.0725 AC: 10944 AN: 151000 Hom.: 1306 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0278

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.000196

Gnomad SAS AF: 0.00168

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.000902

Gnomad OTH AF: 0.0617

GnomAD4 exome AF: 0.0117 AC: 734 AN: 62694 Hom.: 69 Cov.: 0 AF XY: 0.0107 AC XY: 336 AN XY: 31292

Gnomad4 AFR exome AF: 0.228

Gnomad4 AMR exome AF: 0.0212

Gnomad4 ASJ exome AF: 0.0128

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000883

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000794

Gnomad4 OTH exome AF: 0.0238

GnomAD4 genome AF: 0.0727 AC: 10985 AN: 151116 Hom.: 1316 Cov.: 32 AF XY: 0.0702 AC XY: 5184 AN XY: 73826

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.0277

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.000197

Gnomad4 SAS AF: 0.00126

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000902

Gnomad4 OTH AF: 0.0611

Alfa AF: 0.00157 Hom.: 1

Bravo AF: 0.0829

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 25, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.0
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs113297468; hg19: chr6-142623043;