18-48869008-G-A

Variant names:

• chr18-48869008-G-A
• rs7240966

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 0.195 in 152,108 control chromosomes in the GnomAD database, including 2,987 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 0.19 (2987 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 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: 0.195 AC: 29589 AN: 151990 Hom.: 2982 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0352

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.195 AC: 29609 AN: 152108 Hom.: 2987 Cov.: 32 AF XY: 0.190 AC XY: 14100 AN XY: 74344

African (AFR) AF: 0.207 AC: 8602 AN: 41478

American (AMR) AF: 0.153 AC: 2342 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 730 AN: 3472

East Asian (EAS) AF: 0.0351 AC: 182 AN: 5180

South Asian (SAS) AF: 0.104 AC: 500 AN: 4820

European-Finnish (FIN) AF: 0.194 AC: 2053 AN: 10568

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14486 AN: 67998

Other (OTH) AF: 0.208 AC: 440 AN: 2116

Alfa AF: 0.205 Hom.: 9779

Bravo AF: 0.191

Asia WGS AF: 0.0840 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.078
DANN	Benign	0.51
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs7240966; hg19: chr18-46395379;