2-218162249-G-C

Variant names:

• chr2-218162249-G-C
• rs1008562

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 0.408 in 150,330 control chromosomes in the GnomAD database, including 14,252 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 (14252 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 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: 0.408 AC: 61298 AN: 150214 Hom.: 14241 Cov.: 29

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.408 AC: 61309 AN: 150330 Hom.: 14252 Cov.: 29 AF XY: 0.414 AC XY: 30360 AN XY: 73402

African (AFR) AF: 0.209 AC: 8364 AN: 40112

American (AMR) AF: 0.446 AC: 6761 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1202 AN: 3462

East Asian (EAS) AF: 0.717 AC: 3674 AN: 5126

South Asian (SAS) AF: 0.463 AC: 2222 AN: 4804

European-Finnish (FIN) AF: 0.569 AC: 5979 AN: 10508

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.471 AC: 31965 AN: 67856

Other (OTH) AF: 0.386 AC: 806 AN: 2088

Alfa AF: 0.456 Hom.: 9269

Bravo AF: 0.392

Asia WGS AF: 0.563 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.90
DANN	Benign	0.38
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs1008562; hg19: chr2-219026972;