18-51908404-G-A

Variant names:

• chr18-51908404-G-A
• rs10520815

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 0.0918 in 152,170 control chromosomes in the GnomAD database, including 865 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 0.092 (865 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 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: 0.0918 AC: 13963 AN: 152052 Hom.: 866 Cov.: 32

Gnomad AFR AF: 0.0237

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0920

Gnomad ASJ AF: 0.0898

Gnomad EAS AF: 0.00558

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0891

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.0918 AC: 13965 AN: 152170 Hom.: 865 Cov.: 32 AF XY: 0.0892 AC XY: 6639 AN XY: 74388

African (AFR) AF: 0.0237 AC: 983 AN: 41532

American (AMR) AF: 0.0919 AC: 1404 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0898 AC: 311 AN: 3462

East Asian (EAS) AF: 0.00559 AC: 29 AN: 5184

South Asian (SAS) AF: 0.113 AC: 546 AN: 4820

European-Finnish (FIN) AF: 0.0891 AC: 944 AN: 10590

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

European-Non Finnish (NFE) AF: 0.138 AC: 9369 AN: 67994

Other (OTH) AF: 0.112 AC: 237 AN: 2108

Alfa AF: 0.118 Hom.: 2346

Bravo AF: 0.0861

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.2
DANN	Benign	0.60
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10520815; hg19: chr18-49434774;