rs3770303

Positions:

• chr2-153477049-T-C

Variant summary

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

The ENST00000424322.1(ENSG00000227400):​n.430-55086A>G 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 0.817 in 152,136 control chromosomes in the GnomAD database, including 52,014 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 0.82 (52014 hom., cov: 31)
• Consequence: ENST00000424322.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.908 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
	ENST00000424322.1	n.430-55086A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124258 AN: 152018 Hom.: 51960 Cov.: 31

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.973

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.808

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

GnomAD4 genome AF: 0.817 AC: 124364 AN: 152136 Hom.: 52014 Cov.: 31 AF XY: 0.808 AC XY: 60055 AN XY: 74370

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.646

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.836

Gnomad4 OTH AF: 0.805

Alfa AF: 0.813 Hom.: 19736

Bravo AF: 0.809

Asia WGS AF: 0.542 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3770303; hg19: chr2-154333563;