2-238811685-T-C

Variant names:

• chr2-238811685-T-C
• rs9798281

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.971 AC: 40358 AN: 41576

American (AMR) AF: 0.837 AC: 12799 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3148 AN: 3472

East Asian (EAS) AF: 0.729 AC: 3769 AN: 5172

South Asian (SAS) AF: 0.836 AC: 4032 AN: 4822

European-Finnish (FIN) AF: 0.900 AC: 9544 AN: 10610

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61212 AN: 68028

Other (OTH) AF: 0.892 AC: 1884 AN: 2112

Alfa AF: 0.898 Hom.: 27295

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs9798281; hg19: chr2-239720326;