rs3754076

Variant names:

• chr1-36083556-A-G
• rs3754076
• ENST00000446354.3:n.57+420T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-36083556-A-G
• chr1-36083556-A-T

Variant summary

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

The ENST00000446354.3(ENSG00000293245):​n.57+420T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,016 control chromosomes in the GnomAD database, including 46,194 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 0.76 (46194 hom., cov: 32)
• Consequence: ENSG00000293245 ENST00000446354.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 8 publications found

Genes affected

ENSG00000293245 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446354.3. 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
	ENSG00000293245	ENST00000446354.3	TSL:3	n.57+420T>C		intron	N/A
	ENSG00000293245	ENST00000726749.1		n.67+420T>C		intron	N/A
	ENSG00000293245	ENST00000726752.1		n.29+420T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115363 AN: 151898 Hom.: 46190 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.961

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.853

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.909

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.759 AC: 115391 AN: 152016 Hom.: 46194 Cov.: 32 AF XY: 0.756 AC XY: 56155 AN XY: 74306

African (AFR) AF: 0.522 AC: 21611 AN: 41380

American (AMR) AF: 0.706 AC: 10775 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2968 AN: 3472

East Asian (EAS) AF: 0.484 AC: 2493 AN: 5146

South Asian (SAS) AF: 0.853 AC: 4115 AN: 4826

European-Finnish (FIN) AF: 0.835 AC: 8833 AN: 10582

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.909 AC: 61815 AN: 68024

Other (OTH) AF: 0.781 AC: 1647 AN: 2110

Alfa AF: 0.858 Hom.: 238681

Bravo AF: 0.731

Asia WGS AF: 0.704 AC: 2451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.69
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs3754076; hg19: chr1-36549157;