rs3753793

Variant names:

• chr1-85580205-A-C
• rs3753793
• ENST00000609367.2:n.366T>G

Variant summary

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

The ENST00000752544.1(ENSG00000272691):​n.405T>G 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 0.26 in 151,686 control chromosomes in the GnomAD database, including 5,375 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 0.26 (5375 hom., cov: 29)
• Consequence: ENSG00000272691 ENST00000752544.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.835
• Publications: 16 publications found

Genes affected

ENSG00000272691 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752544.1. 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
	ENSG00000272691	ENST00000609367.2	TSL:6	n.366T>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000272691	ENST00000752544.1		n.405T>G		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000272691	ENST00000752545.1		n.41T>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39371 AN: 151566 Hom.: 5363 Cov.: 29

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.260 AC: 39426 AN: 151686 Hom.: 5375 Cov.: 29 AF XY: 0.262 AC XY: 19448 AN XY: 74130

African (AFR) AF: 0.231 AC: 9527 AN: 41318

American (AMR) AF: 0.235 AC: 3594 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1189 AN: 3466

East Asian (EAS) AF: 0.309 AC: 1582 AN: 5122

South Asian (SAS) AF: 0.536 AC: 2573 AN: 4798

European-Finnish (FIN) AF: 0.215 AC: 2262 AN: 10530

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17727 AN: 67882

Other (OTH) AF: 0.280 AC: 588 AN: 2100

Alfa AF: 0.268 Hom.: 18705

Bravo AF: 0.255

Asia WGS AF: 0.404 AC: 1403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	16
DANN	Benign	0.76
PhyloP100		0.83

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: rs3753793;

hg19: chr1-86045888;