2-200848731-T-C

Position:

• chr2-200848731-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 0.798 in 151,308 control chromosomes in the GnomAD database, including 48,300 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 0.80 (48300 hom., cov: 28)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0170

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 (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.200848731T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.798 AC: 120590 AN: 151198 Hom.: 48266 Cov.: 28

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.798 AC: 120686 AN: 151308 Hom.: 48300 Cov.: 28 AF XY: 0.790 AC XY: 58363 AN XY: 73896

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.791

Alfa AF: 0.787 Hom.: 25010

Bravo AF: 0.800

Asia WGS AF: 0.582 AC: 2024 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4674520; hg19: chr2-201713454;