2-231418198-T-C

Position:

• chr2-231418198-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 0.618 in 148,920 control chromosomes in the GnomAD database, including 29,901 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 0.62 (29901 hom., cov: 24)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.231418198T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.618 AC: 91989 AN: 148824 Hom.: 29868 Cov.: 24

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.618 AC: 92068 AN: 148920 Hom.: 29901 Cov.: 24 AF XY: 0.624 AC XY: 45150 AN XY: 72408

Gnomad4 AFR AF: 0.795

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.608

Alfa AF: 0.540 Hom.: 38846

Bravo AF: 0.626

Asia WGS AF: 0.796 AC: 2770 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	5.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6750502; hg19: chr2-232282909;