2-231559006-A-G

Position:

• chr2-231559006-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 0.41 in 152,058 control chromosomes in the GnomAD database, including 13,084 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 0.41 (13084 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 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: 0.410 AC: 62261 AN: 151940 Hom.: 13081 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.410 AC: 62286 AN: 152058 Hom.: 13084 Cov.: 32 AF XY: 0.405 AC XY: 30098 AN XY: 74314

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.378

Alfa AF: 0.409 Hom.: 7815

Bravo AF: 0.410

Asia WGS AF: 0.209 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1667301; hg19: chr2-232423717;