chr2-45355180-A-G

Variant names:

• chr2-45355180-A-G
• rs10167668

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 0.0997 in 152,222 control chromosomes in the GnomAD database, including 889 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 0.10 (889 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.827
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0998 AC: 15178 AN: 152104 Hom.: 891 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0901

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0823

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.0997 AC: 15174 AN: 152222 Hom.: 889 Cov.: 32 AF XY: 0.100 AC XY: 7459 AN XY: 74422

African (AFR) AF: 0.147 AC: 6093 AN: 41526

American (AMR) AF: 0.0901 AC: 1378 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3470

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5178

South Asian (SAS) AF: 0.0578 AC: 279 AN: 4824

European-Finnish (FIN) AF: 0.114 AC: 1211 AN: 10604

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0823 AC: 5596 AN: 68000

Other (OTH) AF: 0.112 AC: 237 AN: 2112

Alfa AF: 0.0873 Hom.: 1091

Bravo AF: 0.0996

Asia WGS AF: 0.0320 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.7
DANN	Benign	0.70
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs10167668; hg19: chr2-45582319;