1-80017721-A-G

Variant names:

• chr1-80017721-A-G
• rs1340682
• ENST00000644002.1:n.459+32825T>C

Variant summary

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

The ENST00000644002.1(ENSG00000285409):​n.459+32825T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,944 control chromosomes in the GnomAD database, including 17,150 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 0.46 (17150 hom., cov: 31)
• Consequence: ENSG00000285409 ENST00000644002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.488
• Publications: 2 publications found

Genes affected

ENSG00000285409 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 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
ENSG00000285409	ENST00000644002.1	n.459+32825T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69403 AN: 151826 Hom.: 17131 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.457 AC: 69464 AN: 151944 Hom.: 17150 Cov.: 31 AF XY: 0.458 AC XY: 33993 AN XY: 74294

African (AFR) AF: 0.658 AC: 27284 AN: 41444

American (AMR) AF: 0.383 AC: 5851 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1650 AN: 3460

East Asian (EAS) AF: 0.390 AC: 2007 AN: 5150

South Asian (SAS) AF: 0.567 AC: 2733 AN: 4816

European-Finnish (FIN) AF: 0.359 AC: 3787 AN: 10544

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24662 AN: 67952

Other (OTH) AF: 0.453 AC: 955 AN: 2108

Alfa AF: 0.408 Hom.: 2345

Bravo AF: 0.465

Asia WGS AF: 0.476 AC: 1655 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	0.28
DANN	Benign	0.34
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1340682; hg19: chr1-80483406;