ENST00000809387.1:n.127-28773C>T

Variant names:

• chr2-49623312-C-T
• rs1391748
• ENST00000809387.1:n.127-28773C>T

Variant summary

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

The ENST00000809387.1(ENSG00000282828):​n.127-28773C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 151,120 control chromosomes in the GnomAD database, including 6,881 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 0.29 (6881 hom., cov: 30)
• Consequence: ENSG00000282828 ENST00000809387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 1 publications found

Genes affected

ENSG00000282828 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906005	XM_047446571.1	c.173+21405C>T		intron_variant	Intron 2 of 3		XP_047302527.1
LOC124906005	XR_007086317.1	n.83-28773C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000282828	ENST00000809387.1	n.127-28773C>T		intron_variant	Intron 1 of 5
ENSG00000282828	ENST00000809388.1	n.255-28773C>T		intron_variant	Intron 1 of 3
ENSG00000282828	ENST00000809389.1	n.83-28773C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.291 AC: 43982 AN: 151006 Hom.: 6870 Cov.: 30

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.291 AC: 44031 AN: 151120 Hom.: 6881 Cov.: 30 AF XY: 0.294 AC XY: 21697 AN XY: 73760

African (AFR) AF: 0.169 AC: 6955 AN: 41142

American (AMR) AF: 0.365 AC: 5530 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1316 AN: 3464

East Asian (EAS) AF: 0.287 AC: 1468 AN: 5108

South Asian (SAS) AF: 0.415 AC: 1987 AN: 4784

European-Finnish (FIN) AF: 0.326 AC: 3367 AN: 10332

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.330 AC: 22359 AN: 67838

Other (OTH) AF: 0.323 AC: 676 AN: 2092

Alfa AF: 0.327 Hom.: 35448

Bravo AF: 0.290

Asia WGS AF: 0.342 AC: 1188 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.49
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1391748; hg19: chr2-49850450;