2-119388079-T-C

Variant names:

• chr2-119388079-T-C
• rs1374313

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 0.551 in 152,094 control chromosomes in the GnomAD database, including 24,281 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 0.55 (24281 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 14 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 (AFR) allele frequency at 95% confidence interval = 0.737 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: 0.551 AC: 83773 AN: 151976 Hom.: 24234 Cov.: 33

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.551 AC: 83873 AN: 152094 Hom.: 24281 Cov.: 33 AF XY: 0.547 AC XY: 40630 AN XY: 74334

African (AFR) AF: 0.744 AC: 30877 AN: 41528

American (AMR) AF: 0.429 AC: 6561 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1720 AN: 3466

East Asian (EAS) AF: 0.378 AC: 1952 AN: 5160

South Asian (SAS) AF: 0.386 AC: 1861 AN: 4824

European-Finnish (FIN) AF: 0.514 AC: 5426 AN: 10554

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.496 AC: 33709 AN: 67966

Other (OTH) AF: 0.523 AC: 1104 AN: 2112

Alfa AF: 0.513 Hom.: 54044

Bravo AF: 0.554

Asia WGS AF: 0.410 AC: 1423 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	0.25
DANN	Benign	0.29
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1374313; hg19: chr2-120145655;