rs3920465

Variant names:

• chr2-35067592-C-A
• rs3920465
• ENST00000453451.5:n.181-91492C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-35067592-C-A
• chr2-35067592-C-G
• chr2-35067592-C-T

Variant summary

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

The ENST00000453451.5(ENSG00000226994):​n.181-91492C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,146 control chromosomes in the GnomAD database, including 1,628 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 0.11 (1628 hom., cov: 32)
• Consequence: ENSG00000226994 ENST00000453451.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

Genes affected

ENSG00000226994 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 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
ENSG00000226994	ENST00000453451.5	n.181-91492C>A		intron_variant	Intron 2 of 5	4
ENSG00000226994	ENST00000585391.5	n.116-91492C>A		intron_variant	Intron 1 of 5	5
ENSG00000226994	ENST00000586769.6	n.158-91492C>A		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16245 AN: 152028 Hom.: 1626 Cov.: 32

Gnomad AFR AF: 0.0266

Gnomad AMI AF: 0.0769

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0983

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0942

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.107 AC: 16247 AN: 152146 Hom.: 1628 Cov.: 32 AF XY: 0.112 AC XY: 8355 AN XY: 74370

Gnomad4 AFR AF: 0.0265

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0983

Gnomad4 NFE AF: 0.0942

Gnomad4 OTH AF: 0.124

Alfa AF: 0.0353 Hom.: 27

Bravo AF: 0.117

Asia WGS AF: 0.350 AC: 1215 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3920465; hg19: chr2-35292658;