ENST00000663591.1:n.399-1122T>C

Variant names:

• chr6-155913388-A-G
• rs9371942
• ENST00000663591.1:n.399-1122T>C

Variant summary

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

The ENST00000663591.1(ENSG00000287092):​n.399-1122T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,132 control chromosomes in the GnomAD database, including 1,310 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 0.11 (1310 hom., cov: 32)
• Consequence: ENSG00000287092 ENST00000663591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928923	XR_001744423.2	n.406-80494T>C		intron_variant	Intron 4 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287092	ENST00000663591.1	n.399-1122T>C		intron_variant	Intron 3 of 3
ENSG00000287092	ENST00000817242.1	n.49-1122T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16808 AN: 152012 Hom.: 1311 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.0447

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0544

Gnomad OTH AF: 0.0943

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

GnomAD4 genome AF: 0.111 AC: 16830 AN: 152132 Hom.: 1310 Cov.: 32 AF XY: 0.113 AC XY: 8404 AN XY: 74360

African (AFR) AF: 0.202 AC: 8385 AN: 41472

American (AMR) AF: 0.113 AC: 1730 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0903 AC: 313 AN: 3468

East Asian (EAS) AF: 0.188 AC: 970 AN: 5152

South Asian (SAS) AF: 0.202 AC: 972 AN: 4816

European-Finnish (FIN) AF: 0.0447 AC: 475 AN: 10616

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0544 AC: 3703 AN: 68014

Other (OTH) AF: 0.0947 AC: 200 AN: 2112

Alfa AF: 0.0710 Hom.: 2388

Bravo AF: 0.114

Asia WGS AF: 0.200 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.64
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs9371942; hg19: chr6-156234522;