2-30040752-A-G

Variant names:

• chr2-30040752-A-G
• rs718153

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 0.772 in 152,140 control chromosomes in the GnomAD database, including 46,209 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 0.77 (46209 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.898 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: 0.772 AC: 117348 AN: 152020 Hom.: 46147 Cov.: 32

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.636

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.696

Gnomad MID AF: 0.702

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.772 AC: 117468 AN: 152140 Hom.: 46209 Cov.: 32 AF XY: 0.774 AC XY: 57574 AN XY: 74356

Gnomad4 AFR AF: 0.906

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.904

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.696

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.743

Alfa AF: 0.722 Hom.: 22699

Bravo AF: 0.787

Asia WGS AF: 0.861 AC: 2994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718153; hg19: chr2-30263618;