2-30222160-T-C

Variant names:

• chr2-30222160-T-C
• rs7579944

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 0.517 in 152,050 control chromosomes in the GnomAD database, including 22,097 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 0.52 (22097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.403
• Publications: 43 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78543 AN: 151932 Hom.: 22094 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.510

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.517 AC: 78571 AN: 152050 Hom.: 22097 Cov.: 32 AF XY: 0.516 AC XY: 38352 AN XY: 74340

African (AFR) AF: 0.285 AC: 11816 AN: 41468

American (AMR) AF: 0.619 AC: 9467 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2338 AN: 3472

East Asian (EAS) AF: 0.357 AC: 1848 AN: 5176

South Asian (SAS) AF: 0.511 AC: 2466 AN: 4824

European-Finnish (FIN) AF: 0.575 AC: 6072 AN: 10568

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42683 AN: 67950

Other (OTH) AF: 0.546 AC: 1151 AN: 2108

Alfa AF: 0.596 Hom.: 126839

Bravo AF: 0.513

Asia WGS AF: 0.428 AC: 1489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.7
DANN	Benign	0.53
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs7579944; hg19: chr2-30445026;