chr18-62425703-A-G

Variant names:

• chr18-62425703-A-G
• rs8094440

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 0.342 in 152,010 control chromosomes in the GnomAD database, including 9,270 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 0.34 (9270 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 7 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 (AFR) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51893 AN: 151892 Hom.: 9250 Cov.: 31

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.342 AC: 51962 AN: 152010 Hom.: 9270 Cov.: 31 AF XY: 0.340 AC XY: 25244 AN XY: 74278

African (AFR) AF: 0.442 AC: 18323 AN: 41436

American (AMR) AF: 0.355 AC: 5424 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1225 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1554 AN: 5168

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4824

European-Finnish (FIN) AF: 0.291 AC: 3075 AN: 10562

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20226 AN: 67962

Other (OTH) AF: 0.345 AC: 726 AN: 2102

Alfa AF: 0.311 Hom.: 12847

Bravo AF: 0.350

Asia WGS AF: 0.312 AC: 1087 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	0.066
DANN	Benign	0.46
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs8094440; hg19: chr18-60092936;