2-150601091-A-G

Variant names:

• chr2-150601091-A-G
• rs2340861
• ENST00000421624.1:n.80-5501T>C

Variant summary

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

The ENST00000421624.1(ENSG00000232359):​n.80-5501T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 152,102 control chromosomes in the GnomAD database, including 38,851 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 0.71 (38851 hom., cov: 33)
• Consequence: ENSG00000232359 ENST00000421624.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

ENSG00000232359 (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 (AFR) allele frequency at 95% confidence interval = 0.777 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
ENSG00000232359	ENST00000421624.1	n.80-5501T>C		intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108245 AN: 151984 Hom.: 38795 Cov.: 33

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.712 AC: 108355 AN: 152102 Hom.: 38851 Cov.: 33 AF XY: 0.710 AC XY: 52784 AN XY: 74344

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.798

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.750

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.736

Alfa AF: 0.702 Hom.: 75782

Bravo AF: 0.714

Asia WGS AF: 0.780 AC: 2712 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	1.7
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2340861; hg19: chr2-151457605;