ENST00000762830.1:n.154+17844A>G

Variant names:

• chr1-100717840-T-C
• rs1409419
• ENST00000762830.1:n.154+17844A>G

Variant summary

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

The ENST00000762830.1(ENSG00000299357):​n.154+17844A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 151,926 control chromosomes in the GnomAD database, including 22,921 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 0.54 (22921 hom., cov: 32)
• Consequence: ENSG00000299357 ENST00000762830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981
• Publications: 20 publications found

Genes affected

ENSG00000299357 (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 (AMR) allele frequency at 95% confidence interval = 0.628 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
ENSG00000299357	ENST00000762830.1	n.154+17844A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.543 AC: 82363 AN: 151808 Hom.: 22893 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.543 AC: 82438 AN: 151926 Hom.: 22921 Cov.: 32 AF XY: 0.546 AC XY: 40541 AN XY: 74242

African (AFR) AF: 0.606 AC: 25102 AN: 41454

American (AMR) AF: 0.639 AC: 9743 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1912 AN: 3468

East Asian (EAS) AF: 0.435 AC: 2237 AN: 5148

South Asian (SAS) AF: 0.559 AC: 2685 AN: 4802

European-Finnish (FIN) AF: 0.507 AC: 5347 AN: 10550

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.494 AC: 33559 AN: 67934

Other (OTH) AF: 0.550 AC: 1159 AN: 2108

Alfa AF: 0.516 Hom.: 28209

Bravo AF: 0.554

Asia WGS AF: 0.516 AC: 1792 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.55
DANN	Benign	0.44
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs1409419; hg19: chr1-101183396;