rs581446

Variant names:

• chr18-10656851-G-A
• rs581446

Your query was ambiguous. Multiple possible variants found:

• chr18-10656851-G-A
• chr18-10656851-G-T

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 0.216 in 151,774 control chromosomes in the GnomAD database, including 4,158 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 0.22 (4158 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.791
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 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: 0.216 AC: 32718 AN: 151656 Hom.: 4143 Cov.: 32

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.216 AC: 32761 AN: 151774 Hom.: 4158 Cov.: 32 AF XY: 0.211 AC XY: 15685 AN XY: 74176

African (AFR) AF: 0.351 AC: 14521 AN: 41376

American (AMR) AF: 0.146 AC: 2235 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3472

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5172

South Asian (SAS) AF: 0.115 AC: 551 AN: 4806

European-Finnish (FIN) AF: 0.152 AC: 1592 AN: 10496

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.185 AC: 12590 AN: 67884

Other (OTH) AF: 0.187 AC: 395 AN: 2108

Alfa AF: 0.188 Hom.: 4335

Bravo AF: 0.221

Asia WGS AF: 0.0770 AC: 269 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.49
DANN	Benign	0.21
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs581446; hg19: chr18-10656848;