chr6-142302091-C-T

Position:

• chr6-142302091-C-T

Variant summary

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

The NM_198569.3(ADGRG6):​c.-239C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0347 in 532,002 control chromosomes in the GnomAD database, including 2,322 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.089 (1849 hom., cov: 32)
  • Exomes 𝑓: 0.013 (473 hom.)
• Consequence: ADGRG6 NM_198569.3 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.566

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=-0.71).
• BP6: Variant 6-142302091-C-T is Benign according to our data. Variant chr6-142302091-C-T is described in ClinVar as [Benign]. Clinvar id is 1221135.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADGRG6	NM_198569.3	c.-239C>T		5_prime_UTR_variant	1/25	ENST00000367609.8	NP_940971.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRG6	ENST00000367609.8	c.-239C>T		5_prime_UTR_variant	1/25	1	NM_198569.3	ENSP00000356581

Frequencies

GnomAD3 genomes AF: 0.0883 AC: 13432 AN: 152094 Hom.: 1840 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0367

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00331

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.00387

Gnomad OTH AF: 0.0774

GnomAD4 exome AF: 0.0132 AC: 5005 AN: 379790 Hom.: 473 Cov.: 3 AF XY: 0.0117 AC XY: 2331 AN XY: 198970

Gnomad4 AFR exome AF: 0.292

Gnomad4 AMR exome AF: 0.0224

Gnomad4 ASJ exome AF: 0.0158

Gnomad4 EAS exome AF: 0.000112

Gnomad4 SAS exome AF: 0.00251

Gnomad4 FIN exome AF: 0.000311

Gnomad4 NFE exome AF: 0.00376

Gnomad4 OTH exome AF: 0.0303

GnomAD4 genome AF: 0.0885 AC: 13475 AN: 152212 Hom.: 1849 Cov.: 32 AF XY: 0.0861 AC XY: 6404 AN XY: 74418

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.0366

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00290

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00387

Gnomad4 OTH AF: 0.0766

Alfa AF: 0.0122 Hom.: 26

Bravo AF: 0.102

Asia WGS AF: 0.0220 AC: 76 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 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	12
DANN	Benign	0.87
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs58392058; hg19: chr6-142623228;