ENST00000758120.1:n.295+38287T>G

Variant names:

• chr5-21233428-A-C
• rs1114626
• ENST00000758120.1:n.295+38287T>G

Variant summary

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

The ENST00000758120.1(ENSG00000249359):​n.295+38287T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.946 in 152,058 control chromosomes in the GnomAD database, including 68,351 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 0.95 (68351 hom., cov: 30)
• Consequence: ENSG00000249359 ENST00000758120.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 1 publications found

Genes affected

ENSG00000249359 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900950	XR_007058710.1	n.622+38287T>G		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249359	ENST00000758120.1	n.295+38287T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.946 AC: 143775 AN: 151940 Hom.: 68298 Cov.: 30

Gnomad AFR AF: 0.868

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.981

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.965

Gnomad FIN AF: 0.994

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.950

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

GnomAD4 genome AF: 0.946 AC: 143882 AN: 152058 Hom.: 68351 Cov.: 30 AF XY: 0.947 AC XY: 70382 AN XY: 74328

African (AFR) AF: 0.868 AC: 35984 AN: 41446

American (AMR) AF: 0.977 AC: 14890 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.981 AC: 3407 AN: 3472

East Asian (EAS) AF: 0.793 AC: 4084 AN: 5152

South Asian (SAS) AF: 0.966 AC: 4652 AN: 4816

European-Finnish (FIN) AF: 0.994 AC: 10536 AN: 10596

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67129 AN: 68006

Other (OTH) AF: 0.946 AC: 2002 AN: 2116

Alfa AF: 0.951 Hom.: 10333

Bravo AF: 0.941

Asia WGS AF: 0.887 AC: 3083 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	1.1
DANN	Benign	0.53
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1114626; hg19: chr5-21233537;