ENST00000762194.1:n.377+1545A>G

Variant names:

• chr4-99401288-T-C
• rs991316
• ENST00000762194.1:n.377+1545A>G

Variant summary

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

The ENST00000762194.1(ENSG00000299279):​n.377+1545A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,868 control chromosomes in the GnomAD database, including 20,763 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 0.51 (20763 hom., cov: 32)
• Consequence: ENSG00000299279 ENST00000762194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.163
• Publications: 30 publications found

Genes affected

ENSG00000299279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762194.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299279	ENST00000762194.1		n.377+1545A>G		intron	N/A
	ENSG00000299279	ENST00000762195.1		n.249+1545A>G		intron	N/A
	ENSG00000299279	ENST00000762196.1		n.492+1545A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78163 AN: 151750 Hom.: 20745 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.515 AC: 78210 AN: 151868 Hom.: 20763 Cov.: 32 AF XY: 0.506 AC XY: 37532 AN XY: 74224

African (AFR) AF: 0.545 AC: 22568 AN: 41422

American (AMR) AF: 0.472 AC: 7210 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1864 AN: 3466

East Asian (EAS) AF: 0.0385 AC: 198 AN: 5138

South Asian (SAS) AF: 0.365 AC: 1760 AN: 4824

European-Finnish (FIN) AF: 0.539 AC: 5663 AN: 10514

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

European-Non Finnish (NFE) AF: 0.548 AC: 37220 AN: 67918

Other (OTH) AF: 0.500 AC: 1055 AN: 2112

Alfa AF: 0.528 Hom.: 77904

Bravo AF: 0.508

Asia WGS AF: 0.236 AC: 823 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.61
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs991316; hg19: chr4-100322445;