2-225146215-C-A

Position:

• chr2-225146215-C-A

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 0.987 in 152,240 control chromosomes in the GnomAD database, including 74,205 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 0.99 (74205 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.99 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: 0.987 AC: 150103 AN: 152122 Hom.: 74150 Cov.: 31

Gnomad AFR AF: 0.998

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.993

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.986

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

GnomAD4 genome AF: 0.987 AC: 150216 AN: 152240 Hom.: 74205 Cov.: 31 AF XY: 0.986 AC XY: 73388 AN XY: 74428

Gnomad4 AFR AF: 0.998

Gnomad4 AMR AF: 0.993

Gnomad4 ASJ AF: 0.984

Gnomad4 EAS AF: 0.801

Gnomad4 SAS AF: 0.989

Gnomad4 FIN AF: 0.989

Gnomad4 NFE AF: 0.992

Gnomad4 OTH AF: 0.985

Alfa AF: 0.989 Hom.: 9861

Bravo AF: 0.986

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.30
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1900871; hg19: chr2-226010932;