chr2-146078690-A-C

Position:

• chr2-146078690-A-C

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 0.0247 in 152,004 control chromosomes in the GnomAD database, including 127 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 0.025 (127 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.96

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0867 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0246 AC: 3732 AN: 151884 Hom.: 127 Cov.: 32

Gnomad AFR AF: 0.00519

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.0875

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.0320

Gnomad SAS AF: 0.0936

Gnomad FIN AF: 0.0220

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0174

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0247 AC: 3747 AN: 152004 Hom.: 127 Cov.: 32 AF XY: 0.0268 AC XY: 1996 AN XY: 74350

Gnomad4 AFR AF: 0.00520

Gnomad4 AMR AF: 0.0878

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.0319

Gnomad4 SAS AF: 0.0939

Gnomad4 FIN AF: 0.0220

Gnomad4 NFE AF: 0.0174

Gnomad4 OTH AF: 0.0304

Alfa AF: 0.0172 Hom.: 4

Bravo AF: 0.0284

Asia WGS AF: 0.0740 AC: 256 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	16
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10195265; hg19: chr2-146836258;