rs3754076

Variant names:

• chr1-36083556-A-G
• rs3754076
• ENST00000446354.2:n.51+420T>C

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446354.2(ENSG00000232862):​n.51+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: ENSG00000232862 ENST00000446354.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

Genes affected

ENSG00000232862 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000232862	ENST00000446354.2	n.51+420T>C		intron_variant	Intron 1 of 2	3

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

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.855

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.909

Gnomad4 OTH AF: 0.781

Alfa AF: 0.879 Hom.: 114421

Bravo AF: 0.731

Asia WGS AF: 0.704 AC: 2451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3754076; hg19: chr1-36549157;