chr1-13828907-G-A

Variant names:

• chr1-13828907-G-A
• rs7520386
• ENST00000801166.1:n.237G>A

Variant summary

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

The ENST00000801166.1(ENSG00000304226):​n.237G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,114 control chromosomes in the GnomAD database, including 21,497 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 0.53 (21497 hom., cov: 33)
• Consequence: ENSG00000304226 ENST00000801166.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 18 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000801166.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304226	ENST00000801166.1		n.237G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000304226	ENST00000801165.1		n.-178G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80597 AN: 151996 Hom.: 21481 Cov.: 33

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.530 AC: 80657 AN: 152114 Hom.: 21497 Cov.: 33 AF XY: 0.530 AC XY: 39397 AN XY: 74392

African (AFR) AF: 0.495 AC: 20547 AN: 41492

American (AMR) AF: 0.513 AC: 7843 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1984 AN: 3472

East Asian (EAS) AF: 0.494 AC: 2553 AN: 5164

South Asian (SAS) AF: 0.425 AC: 2050 AN: 4826

European-Finnish (FIN) AF: 0.569 AC: 6015 AN: 10568

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.557 AC: 37868 AN: 67984

Other (OTH) AF: 0.530 AC: 1118 AN: 2108

Alfa AF: 0.532 Hom.: 10089

Bravo AF: 0.527

Asia WGS AF: 0.482 AC: 1678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.42
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7520386; hg19: chr1-14155402;