2-1773378-A-G

Position:

• chr2-1773378-A-G

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 0.351 in 152,176 control chromosomes in the GnomAD database, including 10,566 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 0.35 (10566 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.808

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53375 AN: 152058 Hom.: 10543 Cov.: 34

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.351 AC: 53450 AN: 152176 Hom.: 10566 Cov.: 34 AF XY: 0.355 AC XY: 26440 AN XY: 74398

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.223

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.318

Alfa AF: 0.288 Hom.: 7815

Bravo AF: 0.348

Asia WGS AF: 0.415 AC: 1442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.071
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6735179; hg19: chr2-1777150;