2-2368409-T-C

Variant names:

• chr2-2368409-T-C
• rs6759198

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.482 in 151,946 control chromosomes in the GnomAD database, including 17,995 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 0.48 (17995 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.701
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.705 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: 0.481 AC: 73073 AN: 151828 Hom.: 17946 Cov.: 31

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.725

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.482 AC: 73183 AN: 151946 Hom.: 17995 Cov.: 31 AF XY: 0.493 AC XY: 36603 AN XY: 74260

African (AFR) AF: 0.455 AC: 18851 AN: 41456

American (AMR) AF: 0.536 AC: 8170 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1357 AN: 3470

East Asian (EAS) AF: 0.724 AC: 3738 AN: 5162

South Asian (SAS) AF: 0.691 AC: 3329 AN: 4816

European-Finnish (FIN) AF: 0.583 AC: 6143 AN: 10532

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30313 AN: 67944

Other (OTH) AF: 0.464 AC: 981 AN: 2116

Alfa AF: 0.457 Hom.: 54194

Bravo AF: 0.474

Asia WGS AF: 0.717 AC: 2490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.48
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs6759198; hg19: chr2-2372181;