2-232378127-T-C

Position:

• chr2-232378127-T-C

Variant summary

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

The variant allele was found at a frequency of 0.487 in 152,126 control chromosomes in the GnomAD database, including 18,739 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 0.49 (18739 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.232378127T>C		intergenic_region
LOC124906123	XR_007088121.1	n.88+818A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74076 AN: 152006 Hom.: 18716 Cov.: 34

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.487 AC: 74127 AN: 152126 Hom.: 18739 Cov.: 34 AF XY: 0.494 AC XY: 36733 AN XY: 74372

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.583

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.602

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.497

Alfa AF: 0.503 Hom.: 3248

Bravo AF: 0.482

Asia WGS AF: 0.653 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3762524; hg19: chr2-233242837;