ENST00000587816.2:c.-397-36761T>C

Variant names:

• chr6-112308352-T-C
• rs1935683
• ENST00000587816.2:c.-397-36761T>C

Variant summary

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

The ENST00000587816.2(ENSG00000281613):​c.-397-36761T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,162 control chromosomes in the GnomAD database, including 1,861 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 0.14 (1861 hom., cov: 32)
• Consequence: ENSG00000281613 ENST00000587816.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

ENSG00000281613 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000281613	ENST00000587816.2	c.-397-36761T>C		intron_variant	Intron 1 of 4	5		ENSP00000487146.1
ENSG00000281613	ENST00000585611.5	c.-731-35046T>C		intron_variant	Intron 1 of 4	5		ENSP00000486440.1
ENSG00000281613	ENST00000590673.5	c.-350-38940T>C		intron_variant	Intron 1 of 3	5		ENSP00000486934.1
ENSG00000281613	ENST00000585504.5	n.112-35046T>C		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21380 AN: 152044 Hom.: 1855 Cov.: 32

Gnomad AFR AF: 0.0604

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.141 AC: 21406 AN: 152162 Hom.: 1861 Cov.: 32 AF XY: 0.140 AC XY: 10444 AN XY: 74390

Gnomad4 AFR AF: 0.0604

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.158

Alfa AF: 0.160 Hom.: 328

Bravo AF: 0.152

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	2.9
DANN	Benign	0.91

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: rs1935683; hg19: chr6-112629554;