1-13864174-A-G

Variant names:

• chr1-13864174-A-G
• rs720035
• ENST00000801165.1:n.232-8369A>G

Variant summary

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

The ENST00000801165.1(ENSG00000304226):​n.232-8369A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 150,982 control chromosomes in the GnomAD database, including 29,733 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 0.62 (29733 hom., cov: 28)
• Consequence: ENSG00000304226 ENST00000801165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 3 publications found

Genes affected

ENSG00000304226 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000801165.1. 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
	ENSG00000304226	ENST00000801165.1		n.232-8369A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.620 AC: 93520 AN: 150864 Hom.: 29700 Cov.: 28

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.689

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.685

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.620 AC: 93608 AN: 150982 Hom.: 29733 Cov.: 28 AF XY: 0.621 AC XY: 45776 AN XY: 73656

African (AFR) AF: 0.460 AC: 18845 AN: 40998

American (AMR) AF: 0.683 AC: 10379 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1830 AN: 3468

East Asian (EAS) AF: 0.748 AC: 3823 AN: 5110

South Asian (SAS) AF: 0.689 AC: 3306 AN: 4796

European-Finnish (FIN) AF: 0.669 AC: 6857 AN: 10248

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.684 AC: 46451 AN: 67862

Other (OTH) AF: 0.633 AC: 1337 AN: 2112

Alfa AF: 0.666 Hom.: 145275

Bravo AF: 0.613

Asia WGS AF: 0.686 AC: 2386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.76
PhyloP100		-0.056

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs720035;

hg19: chr1-14190669;