ENST00000826376.1:n.664+2388A>G

Variant names:

• chr5-159260145-T-C
• rs11744690
• ENST00000826376.1:n.664+2388A>G

Variant summary

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

The ENST00000826376.1(ENSG00000288764):​n.664+2388A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,152 control chromosomes in the GnomAD database, including 6,429 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 0.28 (6429 hom., cov: 32)
• Consequence: ENSG00000288764 ENST00000826376.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 6 publications found

Genes affected

ENSG00000288764 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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
ENSG00000288764	ENST00000826376.1	n.664+2388A>G		intron_variant	Intron 1 of 1
ENSG00000288764	ENST00000826377.1	n.672-826A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42917 AN: 152034 Hom.: 6431 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.282 AC: 42925 AN: 152152 Hom.: 6429 Cov.: 32 AF XY: 0.286 AC XY: 21258 AN XY: 74394

African (AFR) AF: 0.191 AC: 7935 AN: 41530

American (AMR) AF: 0.278 AC: 4251 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 957 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1646 AN: 5160

South Asian (SAS) AF: 0.322 AC: 1553 AN: 4824

European-Finnish (FIN) AF: 0.360 AC: 3809 AN: 10572

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21798 AN: 67988

Other (OTH) AF: 0.251 AC: 529 AN: 2108

Alfa AF: 0.299 Hom.: 22960

Bravo AF: 0.269

Asia WGS AF: 0.284 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.57
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs11744690; hg19: chr5-158687153;