2-190868631-A-T

Variant names:

• chr2-190868631-A-T
• rs7578618

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 0.437 in 152,076 control chromosomes in the GnomAD database, including 16,421 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 0.44 (16421 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 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: 0.436 AC: 66321 AN: 151958 Hom.: 16390 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.678

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.437 AC: 66402 AN: 152076 Hom.: 16421 Cov.: 32 AF XY: 0.432 AC XY: 32157 AN XY: 74370

Gnomad4 AFR AF: 0.641

Gnomad4 AMR AF: 0.514

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.425

Alfa AF: 0.373 Hom.: 1501

Bravo AF: 0.470

Asia WGS AF: 0.506 AC: 1761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.15
DANN	Benign	0.13

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7578618; hg19: chr2-191733357;