2-238811685-T-C

Position:

• chr2-238811685-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.905 in 152,292 control chromosomes in the GnomAD database, including 62,678 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 0.91 (62678 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.238811685T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.905 AC: 137772 AN: 152174 Hom.: 62624 Cov.: 33

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.905 AC: 137888 AN: 152292 Hom.: 62678 Cov.: 33 AF XY: 0.903 AC XY: 67263 AN XY: 74460

Gnomad4 AFR AF: 0.971

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.900

Gnomad4 NFE AF: 0.900

Gnomad4 OTH AF: 0.892

Alfa AF: 0.898 Hom.: 24163

Bravo AF: 0.904

Asia WGS AF: 0.803 AC: 2794 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	12
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9798281; hg19: chr2-239720326;