6-68627895-A-G

Position:

• chr6-68627895-A-G

Variant summary

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

The ENST00000663846.2(ADGRB3-DT):​n.4329T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 152,214 control chromosomes in the GnomAD database, including 62,378 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 0.90 (62378 hom., cov: 31)
• Consequence: ADGRB3-DT ENST00000663846.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276

Genes affected

ADGRB3-DT (HGNC:55774): (ADGRB3 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADGRB3-DT	ENST00000663846.2	n.4329T>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.904 AC: 137478 AN: 152096 Hom.: 62317 Cov.: 31

Gnomad AFR AF: 0.965

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.921

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.865

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.904 AC: 137599 AN: 152214 Hom.: 62378 Cov.: 31 AF XY: 0.905 AC XY: 67307 AN XY: 74410

Gnomad4 AFR AF: 0.965

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.921

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.865

Gnomad4 OTH AF: 0.874

Alfa AF: 0.873 Hom.: 67685

Bravo AF: 0.907

Asia WGS AF: 0.963 AC: 3349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2585617; hg19: chr6-69337787;