ENST00000663591.1:n.399-94483T>C

Variant names:

• chr6-156006749-A-G
• rs1375713
• ENST00000663591.1:n.399-94483T>C

Variant summary

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

The ENST00000663591.1(ENSG00000287092):​n.399-94483T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 151,926 control chromosomes in the GnomAD database, including 31,281 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 0.63 (31281 hom., cov: 32)
• Consequence: ENSG00000287092 ENST00000663591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 1 publications found

Genes affected

ENSG00000287092 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663591.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287092	ENST00000663591.1		n.399-94483T>C		intron	N/A
	ENSG00000301010	ENST00000775499.1		n.365-750A>G		intron	N/A
	ENSG00000301010	ENST00000775500.1		n.302-750A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96317 AN: 151808 Hom.: 31243 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.635 AC: 96410 AN: 151926 Hom.: 31281 Cov.: 32 AF XY: 0.636 AC XY: 47230 AN XY: 74302

African (AFR) AF: 0.777 AC: 32207 AN: 41452

American (AMR) AF: 0.558 AC: 8509 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1947 AN: 3466

East Asian (EAS) AF: 0.592 AC: 3054 AN: 5158

South Asian (SAS) AF: 0.634 AC: 3048 AN: 4808

European-Finnish (FIN) AF: 0.674 AC: 7132 AN: 10588

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38504 AN: 67906

Other (OTH) AF: 0.588 AC: 1239 AN: 2106

Alfa AF: 0.588 Hom.: 13530

Bravo AF: 0.633

Asia WGS AF: 0.631 AC: 2199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.69
PhyloP100		-0.069

Splicing

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

Other links and lift over

dbSNP: rs1375713; hg19: chr6-156327883; COSMIC: COSV60296059;