2-151018421-A-C

Position:

• chr2-151018421-A-C

Variant summary

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

The ENST00000409243.1(ENSG00000222031):​n.298+15388T>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 0.842 in 152,074 control chromosomes in the GnomAD database, including 55,262 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 0.84 (55262 hom., cov: 31)
• Consequence: ENST00000409243.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

Genes affected

(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 (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000409243.1	n.298+15388T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128001 AN: 151958 Hom.: 55221 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.886

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.961

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.842 AC: 128094 AN: 152074 Hom.: 55262 Cov.: 31 AF XY: 0.846 AC XY: 62858 AN XY: 74340

Gnomad4 AFR AF: 0.638

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.886

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.961

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.861

Alfa AF: 0.895 Hom.: 27906

Bravo AF: 0.831

Asia WGS AF: 0.870 AC: 3027 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	6.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4664883; hg19: chr2-151874935;