rs3920465

chr2-35067592-C-Achr2-35067592-C-Gchr2-35067592-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, non coding transcript 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: ENST00000453451.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.145

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000453451.5	n.181-91492C>A		intron_variant, non_coding_transcript_variant		4

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;