rs2301368

Variant names:

• chr17-27803092-G-A
• rs2301368
• ENST00000582441.1:c.438+1031C>T

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.438+1031C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 137,084 control chromosomes in the GnomAD database, including 28,333 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 0.64 (28333 hom., cov: 21)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 3 publications found

Genes affected

ENSG00000266202 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.689 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
ENSG00000266202	ENST00000582441.1	c.438+1031C>T		intron_variant	Intron 4 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.644 AC: 88254 AN: 137040 Hom.: 28318 Cov.: 21

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.650

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

GnomAD4 genome AF: 0.644 AC: 88290 AN: 137084 Hom.: 28333 Cov.: 21 AF XY: 0.649 AC XY: 42496 AN XY: 65504

African (AFR) AF: 0.696 AC: 25553 AN: 36712

American (AMR) AF: 0.690 AC: 9041 AN: 13096

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2509 AN: 3366

East Asian (EAS) AF: 0.532 AC: 2421 AN: 4548

South Asian (SAS) AF: 0.708 AC: 3007 AN: 4248

European-Finnish (FIN) AF: 0.594 AC: 4606 AN: 7754

Middle Eastern (MID) AF: 0.737 AC: 202 AN: 274

European-Non Finnish (NFE) AF: 0.607 AC: 39067 AN: 64330

Other (OTH) AF: 0.650 AC: 1221 AN: 1878

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.642

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.19
DANN	Benign	0.31
PhyloP100		-1.5

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: rs2301368; hg19: chr17-26130118;