rs2301369

Variant names:

• chr17-27802970-G-C
• rs2301369
• ENST00000582441.1:c.438+1153C>G

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.438+1153C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,472 control chromosomes in the GnomAD database, including 11,710 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 0.39 (11710 hom., cov: 29)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 6 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.439 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+1153C>G		intron_variant	Intron 4 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58510 AN: 151354 Hom.: 11704 Cov.: 29

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.387 AC: 58562 AN: 151472 Hom.: 11710 Cov.: 29 AF XY: 0.381 AC XY: 28202 AN XY: 73950

African (AFR) AF: 0.444 AC: 18310 AN: 41200

American (AMR) AF: 0.347 AC: 5279 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1866 AN: 3468

East Asian (EAS) AF: 0.166 AC: 854 AN: 5154

South Asian (SAS) AF: 0.304 AC: 1456 AN: 4794

European-Finnish (FIN) AF: 0.328 AC: 3421 AN: 10436

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25840 AN: 67884

Other (OTH) AF: 0.401 AC: 843 AN: 2104

Alfa AF: 0.382 Hom.: 1236

Bravo AF: 0.395

Asia WGS AF: 0.224 AC: 779 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.68
PhyloP100		0.36

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: rs2301369; hg19: chr17-26129996;