ENST00000419168.2:n.201+256C>T

Variant names:

• chr6-146597814-G-A
• rs2275606
• ENST00000419168.2:n.201+256C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000419168.2(ADGB-DT):​n.201+256C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0804 in 152,206 control chromosomes in the GnomAD database, including 629 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 0.080 (629 hom., cov: 32)
• Consequence: ADGB-DT ENST00000419168.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 24 publications found

Genes affected

ADGB-DT (HGNC:55654): (ADGB divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000419168.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGB-DT	NR_125860.1		n.201+256C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ADGB-DT	ENST00000419168.2	TSL:1	n.201+256C>T		intron	N/A
	ADGB-DT	ENST00000809833.1		n.206+256C>T		intron	N/A
	ADGB-DT	ENST00000809834.1		n.205+256C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0805 AC: 12237 AN: 152088 Hom.: 632 Cov.: 32

Gnomad AFR AF: 0.0798

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0665

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0684

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0804 AC: 12230 AN: 152206 Hom.: 629 Cov.: 32 AF XY: 0.0818 AC XY: 6090 AN XY: 74406

African (AFR) AF: 0.0798 AC: 3314 AN: 41536

American (AMR) AF: 0.0663 AC: 1014 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3472

East Asian (EAS) AF: 0.245 AC: 1265 AN: 5158

South Asian (SAS) AF: 0.152 AC: 733 AN: 4830

European-Finnish (FIN) AF: 0.0600 AC: 636 AN: 10596

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.0685 AC: 4655 AN: 68004

Other (OTH) AF: 0.103 AC: 219 AN: 2116

Alfa AF: 0.0764 Hom.: 2205

Bravo AF: 0.0808

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.21
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs2275606; hg19: chr6-146918950; COSMIC: COSV58856789;