15-90306286-T-G

Variant names:

• chr15-90306286-T-G
• rs6496649
• ENST00000622269.1:c.*3-8012T>G

Variant summary

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

The ENST00000622269.1(ENSG00000275674):​c.*3-8012T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,074 control chromosomes in the GnomAD database, including 29,547 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 0.60 (29547 hom., cov: 32)
• Consequence: ENSG00000275674 ENST00000622269.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366
• Publications: 8 publications found

Genes affected

ENSG00000275674 (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 = 0.84 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
ENSG00000275674	ENST00000622269.1	c.*3-8012T>G		intron_variant	Intron 3 of 3	3		ENSP00000479373.1

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91261 AN: 151956 Hom.: 29504 Cov.: 32

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.601 AC: 91358 AN: 152074 Hom.: 29547 Cov.: 32 AF XY: 0.598 AC XY: 44487 AN XY: 74334

African (AFR) AF: 0.847 AC: 35155 AN: 41506

American (AMR) AF: 0.603 AC: 9215 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1485 AN: 3472

East Asian (EAS) AF: 0.740 AC: 3833 AN: 5178

South Asian (SAS) AF: 0.613 AC: 2952 AN: 4814

European-Finnish (FIN) AF: 0.448 AC: 4723 AN: 10554

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32139 AN: 67954

Other (OTH) AF: 0.574 AC: 1211 AN: 2108

Alfa AF: 0.517 Hom.: 65044

Bravo AF: 0.624

Asia WGS AF: 0.645 AC: 2242 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	2.9
DANN	Benign	0.51
PhyloP100		-0.37

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

Other links and lift over

dbSNP: rs6496649; hg19: chr15-90849518;