2-30388682-G-C

Variant names:

• chr2-30388682-G-C
• rs10514769

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.15 in 152,116 control chromosomes in the GnomAD database, including 1,936 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 0.15 (1936 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.184 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: 0.150 AC: 22833 AN: 151996 Hom.: 1936 Cov.: 32

Gnomad AFR AF: 0.0914

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.0582

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.150 AC: 22834 AN: 152116 Hom.: 1936 Cov.: 32 AF XY: 0.150 AC XY: 11172 AN XY: 74340

African (AFR) AF: 0.0915 AC: 3796 AN: 41496

American (AMR) AF: 0.122 AC: 1861 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3472

East Asian (EAS) AF: 0.0582 AC: 300 AN: 5158

South Asian (SAS) AF: 0.153 AC: 737 AN: 4818

European-Finnish (FIN) AF: 0.200 AC: 2109 AN: 10562

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12664 AN: 67996

Other (OTH) AF: 0.161 AC: 339 AN: 2110

Alfa AF: 0.168 Hom.: 304

Bravo AF: 0.140

Asia WGS AF: 0.0950 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.46
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10514769; hg19: chr2-30611548;